rs142006153
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_018706.7(DHTKD1):c.1550C>T(p.Ala517Val) variant causes a missense change. The variant allele was found at a frequency of 0.000604 in 1,614,216 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A517A) has been classified as Likely benign.
Frequency
Consequence
NM_018706.7 missense
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 | UniProt |
---|---|---|---|---|---|---|---|
DHTKD1 | NM_018706.7 | c.1550C>T | p.Ala517Val | missense_variant | 8/17 | ENST00000263035.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DHTKD1 | ENST00000263035.9 | c.1550C>T | p.Ala517Val | missense_variant | 8/17 | 1 | NM_018706.7 | P1 | |
DHTKD1 | ENST00000448829.1 | c.206C>T | p.Ala69Val | missense_variant | 2/6 | 5 | |||
DHTKD1 | ENST00000465617.1 | n.690C>T | non_coding_transcript_exon_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000788 AC: 120AN: 152210Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00289 AC: 726AN: 251456Hom.: 4 AF XY: 0.00216 AC XY: 294AN XY: 135902
GnomAD4 exome AF: 0.000583 AC: 853AN: 1461888Hom.: 4 Cov.: 31 AF XY: 0.000484 AC XY: 352AN XY: 727248
GnomAD4 genome ? AF: 0.000801 AC: 122AN: 152328Hom.: 1 Cov.: 32 AF XY: 0.000712 AC XY: 53AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Mar 06, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Mar 02, 2022 | - - |
2-aminoadipic 2-oxoadipic aciduria Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
DHTKD1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 10, 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at