chr2-162384777-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_033272.4(KCNH7):āc.2873G>Cā(p.Gly958Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.013 in 1,612,714 control chromosomes in the GnomAD database, including 1,803 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_033272.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNH7 | NM_033272.4 | c.2873G>C | p.Gly958Ala | missense_variant | 13/16 | ENST00000332142.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNH7 | ENST00000332142.10 | c.2873G>C | p.Gly958Ala | missense_variant | 13/16 | 1 | NM_033272.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0620 AC: 9412AN: 151744Hom.: 929 Cov.: 32
GnomAD3 exomes AF: 0.0188 AC: 4706AN: 250650Hom.: 384 AF XY: 0.0144 AC XY: 1954AN XY: 135452
GnomAD4 exome AF: 0.00792 AC: 11568AN: 1460852Hom.: 871 Cov.: 31 AF XY: 0.00707 AC XY: 5140AN XY: 726750
GnomAD4 genome AF: 0.0621 AC: 9430AN: 151862Hom.: 932 Cov.: 32 AF XY: 0.0600 AC XY: 4453AN XY: 74214
ClinVar
Submissions by phenotype
KCNH7-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 23, 2019 | This variant is classified as 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