13-94445735-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000446125.1(DCT):c.1262C>T(p.Pro421Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000258 in 1,588,626 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000446125.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCT | NM_001922.5 | c.1180-2098C>T | intron_variant | ENST00000377028.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCT | ENST00000446125.1 | c.1262C>T | p.Pro421Leu | missense_variant | 8/10 | 1 | |||
DCT | ENST00000377028.10 | c.1180-2098C>T | intron_variant | 1 | NM_001922.5 | P1 | |||
DCT | ENST00000483392.6 | c.636C>T | p.Pro212= | synonymous_variant, NMD_transcript_variant | 6/9 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000947 AC: 2AN: 211128Hom.: 0 AF XY: 0.0000176 AC XY: 2AN XY: 113366
GnomAD4 exome AF: 0.0000272 AC: 39AN: 1436398Hom.: 0 Cov.: 29 AF XY: 0.0000239 AC XY: 17AN XY: 711946
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74384
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 29, 2023 | The c.1262C>T (p.P421L) alteration is located in exon 8 (coding exon 8) of the DCT gene. This alteration results from a C to T substitution at nucleotide position 1262, causing the proline (P) at amino acid position 421 to be replaced by a leucine (L). 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