3-47849627-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_138615.3(DHX30):c.3192-3T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000654 in 1,614,082 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_138615.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000670 AC: 102AN: 152174Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00122 AC: 306AN: 251312Hom.: 0 AF XY: 0.00111 AC XY: 151AN XY: 135842
GnomAD4 exome AF: 0.000652 AC: 953AN: 1461790Hom.: 6 Cov.: 34 AF XY: 0.000631 AC XY: 459AN XY: 727200
GnomAD4 genome AF: 0.000670 AC: 102AN: 152292Hom.: 0 Cov.: 33 AF XY: 0.000618 AC XY: 46AN XY: 74472
ClinVar
Submissions by phenotype
DHX30-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 25, 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 provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2023 | DHX30: BP4, BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at