2-218262736-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6BP7
The NM_170699.3(GPBAR1):c.12C>T(p.Asn4Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000156 in 1,591,254 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_170699.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPBAR1 | ENST00000519574.2 | c.12C>T | p.Asn4Asn | synonymous_variant | Exon 2 of 2 | 1 | NM_170699.3 | ENSP00000430202.1 | ||
GPBAR1 | ENST00000479077.5 | c.12C>T | p.Asn4Asn | synonymous_variant | Exon 2 of 2 | 2 | ENSP00000430698.1 | |||
GPBAR1 | ENST00000521462.1 | c.12C>T | p.Asn4Asn | synonymous_variant | Exon 2 of 2 | 2 | ENSP00000428824.1 | |||
GPBAR1 | ENST00000522678.5 | c.12C>T | p.Asn4Asn | synonymous_variant | Exon 2 of 2 | 2 | ENSP00000430886.1 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152128Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000277 AC: 64AN: 231264Hom.: 1 AF XY: 0.000222 AC XY: 28AN XY: 126306
GnomAD4 exome AF: 0.000155 AC: 223AN: 1439126Hom.: 1 Cov.: 31 AF XY: 0.000160 AC XY: 114AN XY: 712916
GnomAD4 genome AF: 0.000164 AC: 25AN: 152128Hom.: 1 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74296
ClinVar
Submissions by phenotype
GPBAR1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at