chr12-12908347-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_003979.4(GPRC5A):c.98C>T(p.Thr33Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,613,964 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T33T) has been classified as Likely benign.
Frequency
Consequence
NM_003979.4 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 | UniProt |
---|---|---|---|---|---|---|---|
GPRC5A | NM_003979.4 | c.98C>T | p.Thr33Met | missense_variant | 2/4 | ENST00000014914.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPRC5A | ENST00000014914.6 | c.98C>T | p.Thr33Met | missense_variant | 2/4 | 1 | NM_003979.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251340Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135828
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461682Hom.: 0 Cov.: 31 AF XY: 0.0000330 AC XY: 24AN XY: 727152
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 02, 2024 | The c.98C>T (p.T33M) alteration is located in exon 2 (coding exon 1) of the GPRC5A gene. This alteration results from a C to T substitution at nucleotide position 98, causing the threonine (T) at amino acid position 33 to be replaced by a methionine (M). 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