12-12909024-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003979.4(GPRC5A):c.775G>T(p.Ala259Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000756 in 1,613,502 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003979.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPRC5A | NM_003979.4 | c.775G>T | p.Ala259Ser | missense_variant | 2/4 | ENST00000014914.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPRC5A | ENST00000014914.6 | c.775G>T | p.Ala259Ser | missense_variant | 2/4 | 1 | NM_003979.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000394 AC: 60AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000132 AC: 33AN: 250858Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135600
GnomAD4 exome AF: 0.0000424 AC: 62AN: 1461202Hom.: 0 Cov.: 32 AF XY: 0.0000344 AC XY: 25AN XY: 726914
GnomAD4 genome ? AF: 0.000394 AC: 60AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.000443 AC XY: 33AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2024 | The c.775G>T (p.A259S) alteration is located in exon 2 (coding exon 1) of the GPRC5A gene. This alteration results from a G to T substitution at nucleotide position 775, causing the alanine (A) at amino acid position 259 to be replaced by a serine (S). 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