rs872346
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_020877.5(DNAH2):c.10169+3G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 1,613,956 control chromosomes in the GnomAD database, including 103,051 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_020877.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAH2 | NM_020877.5 | c.10169+3G>A | splice_region_variant, intron_variant | ENST00000572933.6 | NP_065928.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAH2 | ENST00000572933.6 | c.10169+3G>A | splice_region_variant, intron_variant | 2 | NM_020877.5 | ENSP00000458355.1 | ||||
DNAH2 | ENST00000389173.6 | c.10169+3G>A | splice_region_variant, intron_variant | 2 | ENSP00000373825.2 | |||||
DNAH2 | ENST00000575105.1 | c.1016+3G>A | splice_region_variant, intron_variant | 5 | ENSP00000461726.1 |
Frequencies
GnomAD3 genomes AF: 0.277 AC: 42068AN: 151970Hom.: 6902 Cov.: 31
GnomAD3 exomes AF: 0.280 AC: 70247AN: 251192Hom.: 11693 AF XY: 0.286 AC XY: 38832AN XY: 135772
GnomAD4 exome AF: 0.351 AC: 512761AN: 1461866Hom.: 96143 Cov.: 86 AF XY: 0.347 AC XY: 252292AN XY: 727228
GnomAD4 genome AF: 0.277 AC: 42107AN: 152090Hom.: 6908 Cov.: 31 AF XY: 0.268 AC XY: 19939AN XY: 74346
ClinVar
Submissions by phenotype
DNAH2-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | 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). - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at