5-76298918-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_014979.4(SV2C):c.1627G>A(p.Asp543Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0834 in 1,613,424 control chromosomes in the GnomAD database, including 6,155 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_014979.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SV2C | NM_014979.4 | c.1627G>A | p.Asp543Asn | missense_variant | 10/13 | ENST00000502798.7 | |
LOC105379042 | XR_001742750.2 | n.447-733C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SV2C | ENST00000502798.7 | c.1627G>A | p.Asp543Asn | missense_variant | 10/13 | 1 | NM_014979.4 | P1 | |
ENST00000502589.1 | n.280-12115C>T | intron_variant, non_coding_transcript_variant | 5 | ||||||
SV2C | ENST00000322285.7 | c.1627G>A | p.Asp543Asn | missense_variant | 10/13 | 2 |
Frequencies
GnomAD3 genomes AF: 0.103 AC: 15705AN: 152090Hom.: 866 Cov.: 32
GnomAD3 exomes AF: 0.0945 AC: 23529AN: 248978Hom.: 1355 AF XY: 0.0886 AC XY: 11968AN XY: 135092
GnomAD4 exome AF: 0.0813 AC: 118770AN: 1461216Hom.: 5286 Cov.: 31 AF XY: 0.0793 AC XY: 57652AN XY: 726938
GnomAD4 genome AF: 0.103 AC: 15718AN: 152208Hom.: 869 Cov.: 32 AF XY: 0.106 AC XY: 7896AN XY: 74408
ClinVar
Submissions by phenotype
SV2C-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 01, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at