chr15-40036374-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003134.6(SRP14):āc.370C>Gā(p.Pro124Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.911 in 1,612,888 control chromosomes in the GnomAD database, including 669,823 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003134.6 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 |
---|---|---|---|---|---|---|---|
SRP14 | NM_003134.6 | c.370C>G | p.Pro124Ala | missense_variant | 5/5 | ENST00000267884.11 | |
SRP14 | NM_001309434.1 | c.226C>G | p.Pro76Ala | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRP14 | ENST00000267884.11 | c.370C>G | p.Pro124Ala | missense_variant | 5/5 | 1 | NM_003134.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.899 AC: 136680AN: 151990Hom.: 61479 Cov.: 35
GnomAD3 exomes AF: 0.904 AC: 227301AN: 251320Hom.: 103114 AF XY: 0.904 AC XY: 122852AN XY: 135874
GnomAD4 exome AF: 0.912 AC: 1332618AN: 1460782Hom.: 608307 Cov.: 63 AF XY: 0.912 AC XY: 662410AN XY: 726690
GnomAD4 genome AF: 0.899 AC: 136772AN: 152106Hom.: 61516 Cov.: 35 AF XY: 0.897 AC XY: 66712AN XY: 74360
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at