chr9-2717922-C-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_133497.4(KCNV2):c.183C>G(p.Gly61=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 1,613,780 control chromosomes in the GnomAD database, including 273,511 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. G61G) has been classified as Likely benign.
Frequency
Consequence
NM_133497.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNV2 | NM_133497.4 | c.183C>G | p.Gly61= | synonymous_variant | 1/2 | ENST00000382082.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNV2 | ENST00000382082.4 | c.183C>G | p.Gly61= | synonymous_variant | 1/2 | 1 | NM_133497.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.603 AC: 91541AN: 151872Hom.: 27888 Cov.: 32
GnomAD3 exomes AF: 0.618 AC: 155283AN: 251212Hom.: 49137 AF XY: 0.609 AC XY: 82637AN XY: 135772
GnomAD4 exome AF: 0.576 AC: 842285AN: 1461790Hom.: 245592 Cov.: 67 AF XY: 0.576 AC XY: 418852AN XY: 727182
GnomAD4 genome ? AF: 0.603 AC: 91620AN: 151990Hom.: 27919 Cov.: 32 AF XY: 0.604 AC XY: 44851AN XY: 74286
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 10, 2014 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 10, 2020 | - - |
Cone dystrophy with supernormal rod response Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at