4-15707566-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004334.3(BST1):c.371G>A(p.Arg124His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,612,776 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R124C) has been classified as Benign.
Frequency
Consequence
NM_004334.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BST1 | NM_004334.3 | c.371G>A | p.Arg124His | missense_variant | 3/9 | ENST00000265016.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BST1 | ENST00000265016.9 | c.371G>A | p.Arg124His | missense_variant | 3/9 | 1 | NM_004334.3 | P1 | |
BST1 | ENST00000382346.7 | c.416G>A | p.Arg139His | missense_variant | 4/10 | 5 | |||
BST1 | ENST00000505785.5 | c.59G>A | p.Arg20His | missense_variant | 1/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151796Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251488Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135918
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1460980Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 726848
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151796Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74164
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 13, 2021 | The c.371G>A (p.R124H) alteration is located in exon 3 (coding exon 3) of the BST1 gene. This alteration results from a G to A substitution at nucleotide position 371, causing the arginine (R) at amino acid position 124 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at