chr10-20888214-GA-G
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_006393.3(NEBL):c.259-8delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00259 in 1,403,682 control chromosomes in the GnomAD database, including 44 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: 0.0136 AC: 1539AN: 113342Hom.: 21 Cov.: 31
GnomAD3 exomes AF: 0.00256 AC: 546AN: 213600Hom.: 5 AF XY: 0.00201 AC XY: 233AN XY: 115848
GnomAD4 exome AF: 0.00162 AC: 2096AN: 1290230Hom.: 23 Cov.: 23 AF XY: 0.00153 AC XY: 989AN XY: 646474
GnomAD4 genome AF: 0.0136 AC: 1544AN: 113452Hom.: 21 Cov.: 31 AF XY: 0.0137 AC XY: 751AN XY: 54638
ClinVar
Submissions by phenotype
not specified Benign:3
259-8delT in intron 3 of NEBL: This variant is located outside the conserved +/- 1, 2 region of the splicing consensus sequence, is part of a polyT stretch, and does not alter the sequence of the ROI. It has been identified in 3% (309/9414) of African Chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.b roadinstitute.org/; dbSNP rs71578979). -
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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. -
Primary dilated cardiomyopathy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at