1-151364974-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_003944.4(SELENBP1):c.1208C>T(p.Thr403Met) variant causes a missense change. The variant allele was found at a frequency of 0.00237 in 1,613,852 control chromosomes in the GnomAD database, including 123 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T403K) has been classified as Uncertain significance.
Frequency
Consequence
NM_003944.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SELENBP1 | NM_003944.4 | c.1208C>T | p.Thr403Met | missense_variant | 11/12 | ENST00000368868.10 | |
SELENBP1 | NM_001258289.2 | c.1334C>T | p.Thr445Met | missense_variant | 11/12 | ||
SELENBP1 | NM_001258288.2 | c.1022C>T | p.Thr341Met | missense_variant | 10/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SELENBP1 | ENST00000368868.10 | c.1208C>T | p.Thr403Met | missense_variant | 11/12 | 1 | NM_003944.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00137 AC: 209AN: 152102Hom.: 8 Cov.: 32
GnomAD3 exomes AF: 0.00503 AC: 1257AN: 250120Hom.: 39 AF XY: 0.00680 AC XY: 919AN XY: 135108
GnomAD4 exome AF: 0.00248 AC: 3622AN: 1461632Hom.: 115 Cov.: 31 AF XY: 0.00355 AC XY: 2579AN XY: 727090
GnomAD4 genome AF: 0.00137 AC: 208AN: 152220Hom.: 8 Cov.: 32 AF XY: 0.00214 AC XY: 159AN XY: 74434
ClinVar
Submissions by phenotype
SELENBP1-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | May 15, 2019 | 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