rs373662459

Variant names:

• chr2-127063659-G-A
• rs373662459
• NM_139343.3:c.699-13C>T

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_Strong BP6_Very_Strong BS1

The NM_139343.3(BIN1):​c.699-13C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,612,190 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.000099 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000021 (0 hom.)
• Consequence: BIN1 NM_139343.3 intron
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.110
• Publications: 0 publications found

Genes affected

BIN1 (HGNC:1052): (bridging integrator 1) This gene encodes several isoforms of a nucleocytoplasmic adaptor protein, one of which was initially identified as a MYC-interacting protein with features of a tumor suppressor. Isoforms that are expressed in the central nervous system may be involved in synaptic vesicle endocytosis and may interact with dynamin, synaptojanin, endophilin, and clathrin. Isoforms that are expressed in muscle and ubiquitously expressed isoforms localize to the cytoplasm and nucleus and activate a caspase-independent apoptotic process. Studies in mouse suggest that this gene plays an important role in cardiac muscle development. Alternate splicing of the gene results in several transcript variants encoding different isoforms. Aberrant splice variants expressed in tumor cell lines have also been described. [provided by RefSeq, Mar 2016]

BIN1 Gene-Disease associations (from GenCC):

• myopathy, centronuclear, 2

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
• centronuclear myopathy

  Inheritance: SD Classification: DEFINITIVE Submitted by: ClinGen
• autosomal dominant centronuclear myopathy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• autosomal recessive centronuclear myopathy

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -16 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 2-127063659-G-A is Benign according to our data. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-127063659-G-A is described in CliVar as Likely_benign. Clinvar id is 262479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0000986 (15/152200) while in subpopulation AFR AF = 0.000217 (9/41442). AF 95% confidence interval is 0.000113. There are 0 homozygotes in GnomAd4. There are 4 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BIN1	NM_139343.3	c.699-13C>T		intron_variant	Intron 8 of 18	ENST00000316724.10	NP_647593.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BIN1	ENST00000316724.10	c.699-13C>T		intron_variant	Intron 8 of 18	1	NM_139343.3	ENSP00000316779.5

Frequencies

GnomAD3 genomes AF: 0.0000986 AC: 15 AN: 152200 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000217

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000196

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000203 AC: 5 AN: 246520 AF XY: 0.0000150

Gnomad AFR exome AF: 0.0000639

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000552

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000899

Gnomad OTH exome AF: 0.000165

GnomAD4 exome AF: 0.0000212 AC: 31 AN: 1459990 Hom.: 0 Cov.: 32 AF XY: 0.0000248 AC XY: 18 AN XY: 726234

African (AFR) AF: 0.000179 AC: 6 AN: 33432

American (AMR) AF: 0.00 AC: 0 AN: 44436

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26082

East Asian (EAS) AF: 0.0000758 AC: 3 AN: 39600

South Asian (SAS) AF: 0.0000233 AC: 2 AN: 85900

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53244

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.0000180 AC: 20 AN: 1111182

Other (OTH) AF: 0.00 AC: 0 AN: 60346

GnomAD4 genome AF: 0.0000986 AC: 15 AN: 152200 Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4 AN XY: 74362

African (AFR) AF: 0.000217 AC: 9 AN: 41442

American (AMR) AF: 0.000196 AC: 3 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5198

South Asian (SAS) AF: 0.00 AC: 0 AN: 4834

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10620

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.0000441 AC: 3 AN: 68034

Other (OTH) AF: 0.00 AC: 0 AN: 2092

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.000102

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

-

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Myopathy, centronuclear, 2 Benign:1

Dec 19, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.8
DANN	Benign	0.57
PhyloP100		0.11

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs373662459; hg19: chr2-127821235;