chr7-77355319-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017439.4(GSAP):c.1232C>T(p.Ser411Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000219 in 1,461,108 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017439.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSAP | NM_017439.4 | c.1232C>T | p.Ser411Leu | missense_variant | 16/31 | ENST00000257626.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSAP | ENST00000257626.12 | c.1232C>T | p.Ser411Leu | missense_variant | 16/31 | 1 | NM_017439.4 | P1 | |
GSAP | ENST00000334003.11 | n.1123C>T | non_coding_transcript_exon_variant | 15/19 | 2 | ||||
GSAP | ENST00000449779.5 | n.188C>T | non_coding_transcript_exon_variant | 2/16 | 2 | ||||
GSAP | ENST00000434084.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.0000559 AC: 14AN: 250348Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135336
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461108Hom.: 0 Cov.: 33 AF XY: 0.0000206 AC XY: 15AN XY: 726952
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2023 | The c.1232C>T (p.S411L) alteration is located in exon 16 (coding exon 16) of the GSAP gene. This alteration results from a C to T substitution at nucleotide position 1232, causing the serine (S) at amino acid position 411 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at