chr13-94440055-C-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBS1_Supporting
The NM_001922.5(DCT):c.1403G>T(p.Gly468Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,766 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001922.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCT | NM_001922.5 | c.1403G>T | p.Gly468Val | missense_variant | 8/8 | ENST00000377028.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCT | ENST00000377028.10 | c.1403G>T | p.Gly468Val | missense_variant | 8/8 | 1 | NM_001922.5 | P1 | |
DCT | ENST00000446125.1 | c.1502G>T | p.Gly501Val | missense_variant | 10/10 | 1 | |||
DCT | ENST00000483392.6 | c.*278G>T | 3_prime_UTR_variant, NMD_transcript_variant | 9/9 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000519 AC: 13AN: 250332Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135244
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461498Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 727050
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74452
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2023 | The c.1502G>T (p.G501V) alteration is located in exon 10 (coding exon 10) of the DCT gene. This alteration results from a G to T substitution at nucleotide position 1502, causing the glycine (G) at amino acid position 501 to be replaced by a valine (V). 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