9-136335983-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001145638.3(GPSM1):c.308T>C(p.Met103Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000868 in 1,612,270 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001145638.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPSM1 | NM_001145638.3 | c.308T>C | p.Met103Thr | missense_variant | Exon 3 of 14 | ENST00000440944.6 | NP_001139110.2 | |
GPSM1 | NM_015597.6 | c.308T>C | p.Met103Thr | missense_variant | Exon 3 of 9 | NP_056412.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPSM1 | ENST00000440944.6 | c.308T>C | p.Met103Thr | missense_variant | Exon 3 of 14 | 5 | NM_001145638.3 | ENSP00000392828.1 | ||
GPSM1 | ENST00000616132.4 | c.308T>C | p.Met103Thr | missense_variant | Exon 3 of 9 | 1 | ENSP00000479405.1 | |||
GPSM1 | ENST00000354753.7 | c.404T>C | p.Met135Thr | missense_variant | Exon 3 of 14 | 5 | ENSP00000346797.4 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152104Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248674Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135114
GnomAD4 exome AF: 0.00000822 AC: 12AN: 1460166Hom.: 0 Cov.: 31 AF XY: 0.00000826 AC XY: 6AN XY: 726352
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152104Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74286
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.308T>C (p.M103T) alteration is located in exon 3 (coding exon 3) of the GPSM1 gene. This alteration results from a T to C substitution at nucleotide position 308, causing the methionine (M) at amino acid position 103 to be replaced by a threonine (T). 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