chr3-154276196-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_020865.3(DHX36):c.3002G>A(p.Arg1001Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000676 in 1,612,542 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020865.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DHX36 | ENST00000496811.6 | c.3002G>A | p.Arg1001Gln | missense_variant | Exon 25 of 25 | 1 | NM_020865.3 | ENSP00000417078.1 | ||
DHX36 | ENST00000329463.9 | c.2960G>A | p.Arg987Gln | missense_variant | Exon 25 of 25 | 1 | ENSP00000330113.5 | |||
DHX36 | ENST00000308361.10 | c.2915G>A | p.Arg972Gln | missense_variant | Exon 24 of 24 | 1 | ENSP00000309296.6 | |||
DHX36 | ENST00000495598.1 | n.552G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000329 AC: 50AN: 151994Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000842 AC: 21AN: 249342Hom.: 0 AF XY: 0.0000668 AC XY: 9AN XY: 134782
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1460430Hom.: 0 Cov.: 31 AF XY: 0.0000358 AC XY: 26AN XY: 726448
GnomAD4 genome AF: 0.000329 AC: 50AN: 152112Hom.: 0 Cov.: 31 AF XY: 0.000377 AC XY: 28AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3002G>A (p.R1001Q) alteration is located in exon 25 (coding exon 25) of the DHX36 gene. This alteration results from a G to A substitution at nucleotide position 3002, causing the arginine (R) at amino acid position 1001 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at