chr8-89982865-A-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_002485.5(NBN):c.38-10T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000122 in 1,610,294 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002485.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 151932Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000125 AC: 31AN: 248874Hom.: 0 AF XY: 0.0000965 AC XY: 13AN XY: 134756
GnomAD4 exome AF: 0.000119 AC: 174AN: 1458244Hom.: 1 Cov.: 31 AF XY: 0.000114 AC XY: 83AN XY: 725592
GnomAD4 genome AF: 0.000151 AC: 23AN: 152050Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74352
ClinVar
Submissions by phenotype
Microcephaly, normal intelligence and immunodeficiency Uncertain:1Benign:2
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not provided Uncertain:1Benign:2
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This variant is associated with the following publications: (PMID: 24549055, 26315354) -
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Hereditary cancer-predisposing syndrome Benign:2
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Hereditary cancer Benign:1
This variant is considered likely benign or benign based on one or more of the following: it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease, and/or has normal protein function, and/or has lack of segregation with disease, and/or has been detected in co-occurrence with known pathogenic variant, and/or has lack of disease association in case-control studies, and/or is located in a region inconsistent with a known cause of pathogenicity. -
Hereditary breast ovarian cancer syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at