chr4-15707565-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004334.3(BST1):c.370C>T(p.Arg124Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000465 in 1,613,946 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R124H) has been classified as Uncertain significance.
Frequency
Consequence
NM_004334.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BST1 | NM_004334.3 | c.370C>T | p.Arg124Cys | missense_variant | 3/9 | ENST00000265016.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BST1 | ENST00000265016.9 | c.370C>T | p.Arg124Cys | missense_variant | 3/9 | 1 | NM_004334.3 | P1 | |
BST1 | ENST00000382346.7 | c.415C>T | p.Arg139Cys | missense_variant | 4/10 | 5 | |||
BST1 | ENST00000505785.5 | c.58C>T | p.Arg20Cys | missense_variant | 1/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000599 AC: 91AN: 151990Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00113 AC: 285AN: 251490Hom.: 0 AF XY: 0.00118 AC XY: 161AN XY: 135920
GnomAD4 exome AF: 0.000451 AC: 659AN: 1461840Hom.: 5 Cov.: 32 AF XY: 0.000469 AC XY: 341AN XY: 727222
GnomAD4 genome ? AF: 0.000598 AC: 91AN: 152106Hom.: 2 Cov.: 32 AF XY: 0.000686 AC XY: 51AN XY: 74352
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 13, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at