chr12-11030510-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_176885.2(TAS2R31):c.826C>G(p.Pro276Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,860 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P276R) has been classified as Likely benign.
Frequency
Consequence
NM_176885.2 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 |
---|---|---|---|---|---|---|---|
TAS2R31 | NM_176885.2 | c.826C>G | p.Pro276Ala | missense_variant | 1/1 | ENST00000390675.2 | |
PRH1-TAS2R14 | NM_001316893.2 | c.140+4272C>G | intron_variant | ||||
PRH1-PRR4 | NR_037918.2 | n.477+4272C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAS2R31 | ENST00000390675.2 | c.826C>G | p.Pro276Ala | missense_variant | 1/1 | NM_176885.2 | P1 | ||
ENST00000703543.1 | c.-126+16510C>G | intron_variant | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 40
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250250Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135710
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461860Hom.: 0 Cov.: 135 AF XY: 0.00000550 AC XY: 4AN XY: 727226
GnomAD4 genome ? Cov.: 40
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2021 | 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