chr13-94460093-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001922.5(DCT):c.1177G>A(p.Val393Met) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000616 in 1,461,460 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001922.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCT | NM_001922.5 | c.1177G>A | p.Val393Met | missense_variant, splice_region_variant | 6/8 | ENST00000377028.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCT | ENST00000377028.10 | c.1177G>A | p.Val393Met | missense_variant, splice_region_variant | 6/8 | 1 | NM_001922.5 | P1 | |
DCT | ENST00000446125.1 | c.1177G>A | p.Val393Met | missense_variant, splice_region_variant | 6/10 | 1 | |||
DCT | ENST00000483392.6 | c.607G>A | p.Val203Met | missense_variant, splice_region_variant, NMD_transcript_variant | 5/9 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250786Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135526
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461460Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 726988
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2022 | The c.1177G>A (p.V393M) alteration is located in exon 6 (coding exon 6) of the DCT gene. This alteration results from a G to A substitution at nucleotide position 1177, causing the valine (V) at amino acid position 393 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