1-151364974-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_003944.4(SELENBP1):c.1208C>A(p.Thr403Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,632 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. T403M) has been classified as Benign.
Frequency
Consequence
NM_003944.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SELENBP1 | NM_003944.4 | c.1208C>A | p.Thr403Lys | missense_variant | 11/12 | ENST00000368868.10 | |
SELENBP1 | NM_001258289.2 | c.1334C>A | p.Thr445Lys | missense_variant | 11/12 | ||
SELENBP1 | NM_001258288.2 | c.1022C>A | p.Thr341Lys | missense_variant | 10/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SELENBP1 | ENST00000368868.10 | c.1208C>A | p.Thr403Lys | missense_variant | 11/12 | 1 | NM_003944.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461632Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727090
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 30, 2024 | The c.1208C>A (p.T403K) alteration is located in exon 11 (coding exon 11) of the SELENBP1 gene. This alteration results from a C to A substitution at nucleotide position 1208, causing the threonine (T) at amino acid position 403 to be replaced by a lysine (K). 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
Publications
No publications associated with this variant yet.