2-118846529-CGCCGCCGCCGCCACTGCCGCCGCG-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP3BP6BS1BS2
The NM_001426.4(EN1):c.615_638delCGCGGCGGCAGTGGCGGCGGCGGC(p.Ala206_Ala213del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00165 in 1,219,408 control chromosomes in the GnomAD database, including 35 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001426.4 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00798 AC: 1181AN: 148014Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.000480 AC: 9AN: 18764Hom.: 0 AF XY: 0.000253 AC XY: 3AN XY: 11856
GnomAD4 exome AF: 0.000774 AC: 829AN: 1071286Hom.: 26 AF XY: 0.000688 AC XY: 352AN XY: 511834
GnomAD4 genome AF: 0.00796 AC: 1179AN: 148122Hom.: 9 Cov.: 32 AF XY: 0.00766 AC XY: 553AN XY: 72206
ClinVar
Submissions by phenotype
EN1-related disorder Benign:1
This variant is classified as likely 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