2-218262879-GCTT-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PM4_SupportingBP6_ModerateBS2
The NM_170699.3(GPBAR1):c.160_162delTTC(p.Phe54del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.000211 in 1,613,522 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_170699.3 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPBAR1 | ENST00000519574.2 | c.160_162delTTC | p.Phe54del | conservative_inframe_deletion | Exon 2 of 2 | 1 | NM_170699.3 | ENSP00000430202.1 | ||
GPBAR1 | ENST00000479077.5 | c.160_162delTTC | p.Phe54del | conservative_inframe_deletion | Exon 2 of 2 | 2 | ENSP00000430698.1 | |||
GPBAR1 | ENST00000521462.1 | c.160_162delTTC | p.Phe54del | conservative_inframe_deletion | Exon 2 of 2 | 2 | ENSP00000428824.1 | |||
GPBAR1 | ENST00000522678.5 | c.160_162delTTC | p.Phe54del | conservative_inframe_deletion | Exon 2 of 2 | 2 | ENSP00000430886.1 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00113 AC: 279AN: 247612Hom.: 1 AF XY: 0.000788 AC XY: 106AN XY: 134496
GnomAD4 exome AF: 0.000214 AC: 312AN: 1461316Hom.: 2 AF XY: 0.000166 AC XY: 121AN XY: 726942
GnomAD4 genome AF: 0.000184 AC: 28AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74348
ClinVar
Submissions by phenotype
not specified Benign:1
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GPBAR1-related disorder Benign:1
This variant is classified as 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