16-72112468-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_014003.4(DHX38):āc.3655C>Gā(p.Arg1219Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0000048 in 1,459,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1219C) has been classified as Uncertain significance.
Frequency
Consequence
NM_014003.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DHX38 | NM_014003.4 | c.3655C>G | p.Arg1219Gly | missense_variant | 27/27 | ENST00000268482.8 | |
DHX38 | XM_011523484.3 | c.3655C>G | p.Arg1219Gly | missense_variant | 27/28 | ||
DHX38 | XM_047434985.1 | c.3655C>G | p.Arg1219Gly | missense_variant | 27/28 | ||
DHX38 | XM_017023913.3 | c.3550C>G | p.Arg1184Gly | missense_variant | 26/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DHX38 | ENST00000268482.8 | c.3655C>G | p.Arg1219Gly | missense_variant | 27/27 | 1 | NM_014003.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249304Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134966
GnomAD4 exome AF: 0.00000480 AC: 7AN: 1459832Hom.: 0 Cov.: 31 AF XY: 0.00000551 AC XY: 4AN XY: 726344
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 20, 2022 | This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 1219 of the DHX38 protein (p.Arg1219Gly). This variant is present in population databases (rs772203418, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with DHX38-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at