10-20888214-GAAA-GAAAA
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_006393.3(NEBL):c.259-8dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0182 in 1,389,664 control chromosomes in the GnomAD database, including 1,471 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_006393.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0853 AC: 9660AN: 113292Hom.: 925 Cov.: 31
GnomAD3 exomes AF: 0.0222 AC: 4734AN: 213600Hom.: 265 AF XY: 0.0179 AC XY: 2069AN XY: 115848
GnomAD4 exome AF: 0.0122 AC: 15621AN: 1276262Hom.: 543 Cov.: 23 AF XY: 0.0114 AC XY: 7283AN XY: 639522
GnomAD4 genome AF: 0.0854 AC: 9685AN: 113402Hom.: 928 Cov.: 31 AF XY: 0.0847 AC XY: 4628AN XY: 54608
ClinVar
Submissions by phenotype
not specified Benign:5
c.259-8dup in intron 3 of NEBL: This variant is classified as benign because it has been identified in 23% (4831/20832) of African chromosomes by the Genome Agg regation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs753190853). ACMG/AMP Criteria: BA1. -
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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NEBL-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Primary dilated cardiomyopathy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at