1-151364574-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_003944.4(SELENBP1):c.1388G>T(p.Gly463Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000173 in 1,614,012 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 (★).
Frequency
Consequence
NM_003944.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SELENBP1 | NM_003944.4 | c.1388G>T | p.Gly463Val | missense_variant | Exon 12 of 12 | ENST00000368868.10 | NP_003935.2 | |
SELENBP1 | NM_001258289.2 | c.1514G>T | p.Gly505Val | missense_variant | Exon 12 of 12 | NP_001245218.1 | ||
SELENBP1 | NM_001258288.2 | c.1202G>T | p.Gly401Val | missense_variant | Exon 11 of 11 | NP_001245217.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251332Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135822
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461842Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727224
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1388G>T (p.G463V) alteration is located in exon 12 (coding exon 12) of the SELENBP1 gene. This alteration results from a G to T substitution at nucleotide position 1388, causing the glycine (G) at amino acid position 463 to be replaced by a valine (V). 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