6-30655494-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BS1_SupportingBS2
The NM_003587.5(DHX16):c.2602C>T(p.Arg868Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000732 in 1,613,108 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R868H) has been classified as Uncertain significance.
Frequency
Consequence
NM_003587.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DHX16 | NM_003587.5 | c.2602C>T | p.Arg868Cys | missense_variant | 17/20 | ENST00000376442.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DHX16 | ENST00000376442.8 | c.2602C>T | p.Arg868Cys | missense_variant | 17/20 | 1 | NM_003587.5 | P1 | |
DHX16 | ENST00000376437.9 | c.1159C>T | p.Arg387Cys | missense_variant | 9/12 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 247080Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134568
GnomAD4 exome AF: 0.0000801 AC: 117AN: 1460938Hom.: 0 Cov.: 32 AF XY: 0.0000647 AC XY: 47AN XY: 726780
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74324
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2023 | The c.2602C>T (p.R868C) alteration is located in exon 17 (coding exon 17) of the DHX16 gene. This alteration results from a C to T substitution at nucleotide position 2602, causing the arginine (R) at amino acid position 868 to be replaced by a cysteine (C). 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