chr11-74457235-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_005472.5(KCNE3):c.*17C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00224 in 1,611,564 control chromosomes in the GnomAD database, including 58 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005472.5 3_prime_UTR
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCNE3 | ENST00000310128 | c.*17C>T | 3_prime_UTR_variant | Exon 3 of 3 | 1 | NM_005472.5 | ENSP00000310557.4 | |||
KCNE3 | ENST00000525550 | c.*17C>T | 3_prime_UTR_variant | Exon 2 of 2 | 1 | ENSP00000433633.1 | ||||
ENSG00000254631 | ENST00000533008.1 | n.155-26942G>A | intron_variant | Intron 2 of 3 | 3 | |||||
KCNE3 | ENST00000532569.5 | c.*31C>T | downstream_gene_variant | 4 | ENSP00000431739.1 |
Frequencies
GnomAD3 genomes AF: 0.0116 AC: 1764AN: 152130Hom.: 31 Cov.: 32
GnomAD3 exomes AF: 0.00314 AC: 772AN: 246152Hom.: 5 AF XY: 0.00232 AC XY: 310AN XY: 133630
GnomAD4 exome AF: 0.00126 AC: 1833AN: 1459316Hom.: 27 Cov.: 30 AF XY: 0.00109 AC XY: 790AN XY: 725814
GnomAD4 genome AF: 0.0116 AC: 1769AN: 152248Hom.: 31 Cov.: 32 AF XY: 0.0110 AC XY: 820AN XY: 74450
ClinVar
Submissions by phenotype
not specified Benign:2
- -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at