rs148550258
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_133497.4(KCNV2):c.280G>A(p.Ala94Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000806 in 1,613,044 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A94D) has been classified as Uncertain significance.
Frequency
Consequence
NM_133497.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNV2 | NM_133497.4 | c.280G>A | p.Ala94Thr | missense_variant | 1/2 | ENST00000382082.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNV2 | ENST00000382082.4 | c.280G>A | p.Ala94Thr | missense_variant | 1/2 | 1 | NM_133497.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000138 AC: 34AN: 246666Hom.: 0 AF XY: 0.000180 AC XY: 24AN XY: 133554
GnomAD4 exome AF: 0.0000767 AC: 112AN: 1460874Hom.: 0 Cov.: 81 AF XY: 0.0000867 AC XY: 63AN XY: 726638
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152170Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74328
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at