2-218262758-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_170699.3(GPBAR1):c.34C>T(p.Pro12Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,607,936 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_170699.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPBAR1 | ENST00000519574.2 | c.34C>T | p.Pro12Ser | missense_variant | Exon 2 of 2 | 1 | NM_170699.3 | ENSP00000430202.1 | ||
GPBAR1 | ENST00000479077.5 | c.34C>T | p.Pro12Ser | missense_variant | Exon 2 of 2 | 2 | ENSP00000430698.1 | |||
GPBAR1 | ENST00000521462.1 | c.34C>T | p.Pro12Ser | missense_variant | Exon 2 of 2 | 2 | ENSP00000428824.1 | |||
GPBAR1 | ENST00000522678.5 | c.34C>T | p.Pro12Ser | missense_variant | Exon 2 of 2 | 2 | ENSP00000430886.1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152084Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1455852Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 723514
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152084Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74278
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at