14-96382419-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_016472.5(GSKIP):c.172C>T(p.Arg58Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,612,822 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016472.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GSKIP | NM_016472.5 | c.172C>T | p.Arg58Trp | missense_variant | 3/4 | ENST00000555181.6 | NP_057556.2 | |
GSKIP | NM_001271904.1 | c.172C>T | p.Arg58Trp | missense_variant | 3/4 | NP_001258833.1 | ||
GSKIP | NM_001271905.2 | c.172C>T | p.Arg58Trp | missense_variant | 3/4 | NP_001258834.1 | ||
GSKIP | NM_001271906.2 | c.172C>T | p.Arg58Trp | missense_variant | 2/3 | NP_001258835.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GSKIP | ENST00000555181.6 | c.172C>T | p.Arg58Trp | missense_variant | 3/4 | 1 | NM_016472.5 | ENSP00000450420 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151928Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251428Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135882
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1460894Hom.: 1 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 726812
GnomAD4 genome AF: 0.0000395 AC: 6AN: 151928Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74188
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 28, 2024 | The c.172C>T (p.R58W) alteration is located in exon 2 (coding exon 1) of the GSKIP gene. This alteration results from a C to T substitution at nucleotide position 172, causing the arginine (R) at amino acid position 58 to be replaced by a tryptophan (W). 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