2-50346870-GCGCCGCCGCCGCCGCCGC-GCGC
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_001330092.2(NRXN1):c.65_79delGCGGCGGCGGCGGCG(p.Gly22_Gly26del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00361 in 1,366,786 control chromosomes in the GnomAD database, including 340 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001330092.2 disruptive_inframe_deletion
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: 0.0146 AC: 2202AN: 150380Hom.: 38 Cov.: 32
GnomAD3 exomes AF: 0.00797 AC: 597AN: 74950Hom.: 196 AF XY: 0.00662 AC XY: 293AN XY: 44242
GnomAD4 exome AF: 0.00224 AC: 2726AN: 1216306Hom.: 302 AF XY: 0.00204 AC XY: 1216AN XY: 594990
GnomAD4 genome AF: 0.0147 AC: 2205AN: 150480Hom.: 38 Cov.: 32 AF XY: 0.0141 AC XY: 1038AN XY: 73468
ClinVar
Submissions by phenotype
not specified Benign:1
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Inborn genetic diseases Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
not provided Benign:1
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NRXN1-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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at