3-53888462-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_021237.5(SELENOK):c.41G>A(p.Ser14Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000807 in 1,611,168 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_021237.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SELENOK | ENST00000495461.6 | c.41G>A | p.Ser14Asn | missense_variant | Exon 2 of 5 | 1 | NM_021237.5 | ENSP00000418813.1 | ||
SELENOK | ENST00000485414.1 | n.273G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 5 | |||||
SELENOK | ENST00000487571.1 | n.108G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 | |||||
SELENOK | ENST00000488746.1 | n.41G>A | non_coding_transcript_exon_variant | Exon 2 of 5 | 3 | ENSP00000417272.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152220Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247884Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134632
GnomAD4 exome AF: 0.00000480 AC: 7AN: 1458948Hom.: 0 Cov.: 29 AF XY: 0.00000276 AC XY: 2AN XY: 725940
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74362
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at