NM_170699.3:c.-1G>A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_170699.3(GPBAR1):c.-1G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000444 in 1,578,264 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_170699.3 5_prime_UTR
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 | c.-1G>A | 5_prime_UTR_variant | Exon 2 of 2 | 1 | NM_170699.3 | ENSP00000430202.1 | |||
GPBAR1 | ENST00000479077 | c.-1G>A | 5_prime_UTR_variant | Exon 2 of 2 | 2 | ENSP00000430698.1 | ||||
GPBAR1 | ENST00000521462 | c.-1G>A | 5_prime_UTR_variant | Exon 2 of 2 | 2 | ENSP00000428824.1 | ||||
GPBAR1 | ENST00000522678 | c.-1G>A | 5_prime_UTR_variant | Exon 2 of 2 | 2 | ENSP00000430886.1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000544 AC: 12AN: 220606Hom.: 0 AF XY: 0.0000249 AC XY: 3AN XY: 120368
GnomAD4 exome AF: 0.0000393 AC: 56AN: 1426040Hom.: 0 Cov.: 31 AF XY: 0.0000411 AC XY: 29AN XY: 705092
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74420
ClinVar
Submissions by phenotype
not provided Uncertain:1
- -
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