2-53853756-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_006794.4(GPR75):c.1001G>A(p.Cys334Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C334F) has been classified as Uncertain significance.
Frequency
Consequence
NM_006794.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR75 | NM_006794.4 | c.1001G>A | p.Cys334Tyr | missense_variant | 2/2 | ENST00000394705.3 | |
GPR75-ASB3 | NM_001164165.2 | c.101+6072G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR75 | ENST00000394705.3 | c.1001G>A | p.Cys334Tyr | missense_variant | 2/2 | 1 | NM_006794.4 | P1 | |
ASB3 | ENST00000406625.6 | c.-14+6072G>A | intron_variant | 2 | P1 | ||||
ASB3 | ENST00000459916.1 | n.93+6072G>A | intron_variant, non_coding_transcript_variant | 4 | |||||
ASB3 | ENST00000498475.2 | n.163+6072G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251472Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135920
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 17, 2023 | The c.1001G>A (p.C334Y) alteration is located in exon 2 (coding exon 1) of the GPR75 gene. This alteration results from a G to A substitution at nucleotide position 1001, causing the cysteine (C) at amino acid position 334 to be replaced by a tyrosine (Y). 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