7-77355238-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_017439.4(GSAP):āc.1313A>Gā(p.Gln438Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000586 in 1,613,336 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_017439.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GSAP | ENST00000257626.12 | c.1313A>G | p.Gln438Arg | missense_variant | 16/31 | 1 | NM_017439.4 | ENSP00000257626.7 | ||
GSAP | ENST00000334003.11 | n.1204A>G | non_coding_transcript_exon_variant | 15/19 | 2 | |||||
GSAP | ENST00000434084.1 | n.47A>G | non_coding_transcript_exon_variant | 1/4 | 3 | |||||
GSAP | ENST00000449779.5 | n.269A>G | non_coding_transcript_exon_variant | 2/16 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000493 AC: 75AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000296 AC: 74AN: 249586Hom.: 0 AF XY: 0.000319 AC XY: 43AN XY: 134960
GnomAD4 exome AF: 0.000595 AC: 870AN: 1461018Hom.: 0 Cov.: 30 AF XY: 0.000576 AC XY: 419AN XY: 726858
GnomAD4 genome AF: 0.000492 AC: 75AN: 152318Hom.: 0 Cov.: 32 AF XY: 0.000416 AC XY: 31AN XY: 74494
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2023 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at