rs61729032
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The ENST00000355265.7(KEL):c.1481A>T(p.Glu494Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000747 in 1,613,748 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
ENST00000355265.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KEL | NM_000420.3 | c.1481A>T | p.Glu494Val | missense_variant | 13/19 | ENST00000355265.7 | NP_000411.1 | |
KEL | XM_005249993.2 | c.1517A>T | p.Glu506Val | missense_variant | 13/19 | XP_005250050.1 | ||
KEL | XM_047420357.1 | c.1370A>T | p.Glu457Val | missense_variant | 12/18 | XP_047276313.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KEL | ENST00000355265.7 | c.1481A>T | p.Glu494Val | missense_variant | 13/19 | 1 | NM_000420.3 | ENSP00000347409 | P1 | |
KEL | ENST00000465697.1 | n.342A>T | non_coding_transcript_exon_variant | 2/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00118 AC: 180AN: 152132Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00171 AC: 429AN: 251478Hom.: 0 AF XY: 0.00165 AC XY: 224AN XY: 135914
GnomAD4 exome AF: 0.000702 AC: 1026AN: 1461498Hom.: 7 Cov.: 30 AF XY: 0.000726 AC XY: 528AN XY: 727078
GnomAD4 genome AF: 0.00118 AC: 180AN: 152250Hom.: 1 Cov.: 32 AF XY: 0.00154 AC XY: 115AN XY: 74446
ClinVar
Submissions by phenotype
KEL-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 12, 2019 | This variant is classified as likely 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