chr6-116792738-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_148963.4(GPRC6A):āc.2185A>Gā(p.Thr729Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000359 in 1,613,790 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_148963.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPRC6A | NM_148963.4 | c.2185A>G | p.Thr729Ala | missense_variant | 6/6 | ENST00000310357.8 | NP_683766.2 | |
GPRC6A | NM_001286355.1 | c.1972A>G | p.Thr658Ala | missense_variant | 5/5 | NP_001273284.1 | ||
GPRC6A | NM_001286354.1 | c.1660A>G | p.Thr554Ala | missense_variant | 6/6 | NP_001273283.1 | ||
GPRC6A | XM_017010475.2 | c.2044A>G | p.Thr682Ala | missense_variant | 7/7 | XP_016865964.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPRC6A | ENST00000310357.8 | c.2185A>G | p.Thr729Ala | missense_variant | 6/6 | 1 | NM_148963.4 | ENSP00000309493 | P1 | |
GPRC6A | ENST00000368549.7 | c.1972A>G | p.Thr658Ala | missense_variant | 5/5 | 1 | ENSP00000357537 | |||
GPRC6A | ENST00000530250.1 | c.1660A>G | p.Thr554Ala | missense_variant | 6/6 | 1 | ENSP00000433465 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152134Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000718 AC: 18AN: 250564Hom.: 0 AF XY: 0.0000886 AC XY: 12AN XY: 135372
GnomAD4 exome AF: 0.0000369 AC: 54AN: 1461538Hom.: 0 Cov.: 36 AF XY: 0.0000358 AC XY: 26AN XY: 727020
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152252Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74446
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at