chr4-15715789-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_004334.3(BST1):c.694G>A(p.Gly232Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000695 in 1,583,526 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_004334.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BST1 | NM_004334.3 | c.694G>A | p.Gly232Arg | missense_variant | 6/9 | ENST00000265016.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BST1 | ENST00000265016.9 | c.694G>A | p.Gly232Arg | missense_variant | 6/9 | 1 | NM_004334.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152136Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000432 AC: 98AN: 226850Hom.: 1 AF XY: 0.000374 AC XY: 46AN XY: 123026
GnomAD4 exome AF: 0.0000720 AC: 103AN: 1431390Hom.: 1 Cov.: 30 AF XY: 0.0000689 AC XY: 49AN XY: 711582
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152136Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74314
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 11, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at