13-113822090-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000820.4(GAS6):c.1750G>T(p.Gly584Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000175 in 1,597,256 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_000820.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GAS6 | NM_000820.4 | c.1750G>T | p.Gly584Cys | missense_variant | 14/15 | ENST00000327773.7 | NP_000811.1 | |
GAS6-AS1 | NR_044995.2 | n.82+6399C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GAS6 | ENST00000327773.7 | c.1750G>T | p.Gly584Cys | missense_variant | 14/15 | 1 | NM_000820.4 | ENSP00000331831 | P1 | |
GAS6-AS1 | ENST00000458001.2 | n.62+6399C>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000104 AC: 23AN: 220248Hom.: 0 AF XY: 0.000109 AC XY: 13AN XY: 119284
GnomAD4 exome AF: 0.0000180 AC: 26AN: 1445056Hom.: 0 Cov.: 32 AF XY: 0.0000209 AC XY: 15AN XY: 717226
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 12, 2024 | The c.1750G>T (p.G584C) alteration is located in exon 14 (coding exon 14) of the GAS6 gene. This alteration results from a G to T substitution at nucleotide position 1750, causing the glycine (G) at amino acid position 584 to be replaced by a cysteine (C). 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