9-2729472-AGAC-A
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM2PM4_Supporting
The NM_133497.4(KCNV2):βc.1384_1386delβ(p.Asp462del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,820 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (β β ). Synonymous variant affecting the same amino acid position (i.e. D462D) has been classified as Benign.
Frequency
Consequence
NM_133497.4 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCNV2 | NM_133497.4 | c.1384_1386del | p.Asp462del | inframe_deletion | 2/2 | ENST00000382082.4 | NP_598004.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCNV2 | ENST00000382082.4 | c.1384_1386del | p.Asp462del | inframe_deletion | 2/2 | 1 | NM_133497.4 | ENSP00000371514 | P1 | |
PUM3 | ENST00000490444.2 | c.*127-8943_*127-8941del | intron_variant, NMD_transcript_variant | 5 | ENSP00000474467 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251374Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135856
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461664Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 727150
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 18, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 867088). This variant has not been reported in the literature in individuals affected with KCNV2-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.007%). This variant, c.1384_1386del, results in the deletion of 1 amino acid(s) of the KCNV2 protein (p.Asp462del), but otherwise preserves the integrity of the reading frame. - |
Retinal dystrophy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Blueprint Genetics | Feb 07, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at