11-62876882-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000377890.6(SLC3A2):c.299-4137G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00224 in 1,037,170 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.010 ( 18 hom., cov: 32)
Exomes 𝑓: 0.00086 ( 19 hom. )
Consequence
SLC3A2
ENST00000377890.6 intron
ENST00000377890.6 intron
Scores
2
Splicing: ADA: 0.00002236
2
Clinical Significance
Conservation
PhyloP100: 0.162
Genes affected
SLC3A2 (HGNC:11026): (solute carrier family 3 member 2) This gene is a member of the solute carrier family and encodes a cell surface, transmembrane protein. The protein exists as the heavy chain of a heterodimer, covalently bound through di-sulfide bonds to one of several possible light chains. The encoded transporter plays a role in regulation of intracellular calcium levels and transports L-type amino acids. Alternatively spliced transcript variants, encoding different isoforms, have been characterized. [provided by RefSeq, Nov 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 11-62876882-G-A is Benign according to our data. Variant chr11-62876882-G-A is described in ClinVar as [Benign]. Clinvar id is 781000.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0103 (1565/152240) while in subpopulation AFR AF= 0.0358 (1488/41548). AF 95% confidence interval is 0.0343. There are 18 homozygotes in gnomad4. There are 717 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1566 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC3A2 | NM_001012662.3 | c.301+3G>A | splice_donor_region_variant, intron_variant | ||||
SLC3A2 | NM_001012664.3 | c.113-4137G>A | intron_variant | ||||
SLC3A2 | NM_002394.6 | c.299-4137G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC3A2 | ENST00000377889.6 | c.113-4137G>A | intron_variant | 1 | |||||
SLC3A2 | ENST00000377890.6 | c.299-4137G>A | intron_variant | 1 | |||||
SLC3A2 | ENST00000377891.6 | c.301+3G>A | splice_donor_region_variant, intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0103 AC: 1566AN: 152122Hom.: 18 Cov.: 32
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GnomAD3 exomes AF: 0.000641 AC: 9AN: 14030Hom.: 1 AF XY: 0.000560 AC XY: 5AN XY: 8930
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GnomAD4 exome AF: 0.000861 AC: 762AN: 884930Hom.: 19 Cov.: 21 AF XY: 0.000728 AC XY: 304AN XY: 417442
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: -3
Find out detailed SpliceAI scores and Pangolin per-transcript scores at