17-82037511-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016286.4(DCXR):c.89C>T(p.Thr30Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,541,278 control chromosomes in the GnomAD database, including 1 homozygotes. 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_016286.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DCXR | NM_016286.4 | c.89C>T | p.Thr30Met | missense_variant | Exon 2 of 8 | ENST00000306869.7 | NP_057370.1 | |
DCXR | NM_001195218.1 | c.83C>T | p.Thr28Met | missense_variant | Exon 2 of 8 | NP_001182147.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152212Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000573 AC: 8AN: 139718Hom.: 1 AF XY: 0.0000776 AC XY: 6AN XY: 77272
GnomAD4 exome AF: 0.0000245 AC: 34AN: 1389066Hom.: 1 Cov.: 32 AF XY: 0.0000335 AC XY: 23AN XY: 686670
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152212Hom.: 0 Cov.: 34 AF XY: 0.0000538 AC XY: 4AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.89C>T (p.T30M) alteration is located in exon 2 (coding exon 2) of the DCXR gene. This alteration results from a C to T substitution at nucleotide position 89, causing the threonine (T) at amino acid position 30 to be replaced by a methionine (M). 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