6-32192473-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001276501.2(GPSM3):āc.41A>Cā(p.Gln14Pro) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000000695 in 1,438,654 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001276501.2 missense, splice_region
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPSM3 | NM_001276501.2 | c.41A>C | p.Gln14Pro | missense_variant, splice_region_variant | 1/4 | ENST00000375040.8 | NP_001263430.1 | |
GPSM3 | NM_022107.3 | c.41A>C | p.Gln14Pro | missense_variant, splice_region_variant | 5/8 | NP_071390.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPSM3 | ENST00000375040.8 | c.41A>C | p.Gln14Pro | missense_variant, splice_region_variant | 1/4 | 1 | NM_001276501.2 | ENSP00000364180 | P1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 6.95e-7 AC: 1AN: 1438654Hom.: 0 Cov.: 31 AF XY: 0.00000140 AC XY: 1AN XY: 713290
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2022 | The c.41A>C (p.Q14P) alteration is located in exon 5 (coding exon 1) of the GPSM3 gene. This alteration results from a A to C substitution at nucleotide position 41, causing the glutamine (Q) at amino acid position 14 to be replaced by a proline (P). 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