chr3-70972551-G-A

Variant names:

• chr3-70972551-G-A
• rs572849158
• NM_001349338.3:c.1652+4C>T

Variant summary

Our verdict is Benign. The variant received -18 ACMG points: 0P and 18B. BP4_Moderate BP6_Very_Strong BS1 BS2

The NM_001349338.3(FOXP1):​c.1652+4C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,614,156 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.000026 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000096 (0 hom.)
• Consequence: FOXP1 NM_001349338.3 splice_region, intron
• Scores: Splicing: ADA: 0.0001019
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 1.58
• Publications: 0 publications found

Genes affected

FOXP1 (HGNC:3823): (forkhead box P1) This gene belongs to subfamily P of the forkhead box (FOX) transcription factor family. Forkhead box transcription factors play important roles in the regulation of tissue- and cell type-specific gene transcription during both development and adulthood. Forkhead box P1 protein contains both DNA-binding- and protein-protein binding-domains. This gene may act as a tumor suppressor as it is lost in several tumor types and maps to a chromosomal region (3p14.1) reported to contain a tumor suppressor gene(s). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

FOXP1 Gene-Disease associations (from GenCC):

• intellectual disability-severe speech delay-mild dysmorphism syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Illumina, G2P, ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics
• congenital heart disease

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ENSG00000285708 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -18 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BP6: Variant 3-70972551-G-A is Benign according to our data. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-70972551-G-A is described in CliVar as Likely_benign. Clinvar id is 562027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population eas. GnomAdExome4 allele frequency = 0.00000958 (14/1461876) while in subpopulation EAS AF = 0.000101 (4/39700). AF 95% confidence interval is 0.0000335. There are 0 homozygotes in GnomAdExome4. There are 5 alleles in the male GnomAdExome4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High AC in GnomAdExome4 at 14 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXP1	NM_001349338.3	c.1652+4C>T		splice_region_variant, intron_variant	Intron 18 of 20	ENST00000649528.3	NP_001336267.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXP1	ENST00000649528.3	c.1652+4C>T		splice_region_variant, intron_variant	Intron 18 of 20		NM_001349338.3	ENSP00000497369.1
ENSG00000285708	ENST00000647725.1	c.1652+4C>T		splice_region_variant, intron_variant	Intron 23 of 25			ENSP00000497585.1

Frequencies

GnomAD3 genomes AF: 0.0000263 AC: 4 AN: 152162 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000483

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000654

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000159 AC: 4 AN: 251494 AF XY: 0.0000147

Gnomad AFR exome AF: 0.0000615

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000109

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000879

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000958 AC: 14 AN: 1461876 Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5 AN XY: 727244

African (AFR) AF: 0.00 AC: 0 AN: 33480

American (AMR) AF: 0.00 AC: 0 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.000101 AC: 4 AN: 39700

South Asian (SAS) AF: 0.00 AC: 0 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53420

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5766

European-Non Finnish (NFE) AF: 0.00000719 AC: 8 AN: 1112000

Other (OTH) AF: 0.0000331 AC: 2 AN: 60392

GnomAD4 genome AF: 0.0000263 AC: 4 AN: 152280 Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2 AN XY: 74448

African (AFR) AF: 0.0000481 AC: 2 AN: 41550

American (AMR) AF: 0.0000653 AC: 1 AN: 15308

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10598

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68030

Other (OTH) AF: 0.00 AC: 0 AN: 2110

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000189

ClinVar

Significance: Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Inborn genetic diseases Benign:1

Jan 30, 2017

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

not provided Benign:1

Feb 06, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Intellectual disability Benign:1

Jan 01, 2017

Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille

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	-0.41
CADD	Benign	22
DANN	Benign	0.71
PhyloP100		1.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00010
dbscSNV1_RF	Benign	0.0060
SpliceAI score (max)		0.14		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: rs572849158; hg19: chr3-71021702; COSMIC: COSV59557469;