rs752839237
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_147127.5(EVC2):c.3879_3881delGAA(p.Lys1293del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000052 in 1,614,178 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_147127.5 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000237 AC: 36AN: 152208Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 30AN: 251448Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135894
GnomAD4 exome AF: 0.0000328 AC: 48AN: 1461852Hom.: 0 AF XY: 0.0000358 AC XY: 26AN XY: 727230
GnomAD4 genome AF: 0.000236 AC: 36AN: 152326Hom.: 1 Cov.: 32 AF XY: 0.000295 AC XY: 22AN XY: 74480
ClinVar
Submissions by phenotype
Ellis-van Creveld syndrome Uncertain:1
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not provided Uncertain:1
The EVC2 c.3879_3881del; p.Lys1293del variant (rs752839237), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 550613). This variant is found in the Latino/Admixed American population with an allele frequency of 0.07% (25/35434 alleles) in the Genome Aggregation Database. This variant deletes a single lysine residue leaving the rest of the protein in-frame. Due to limited information, the clinical significance of this variant is uncertain at this time. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at