rs3782974

Positions:

• chr13-94440642-T-A
• chr13-94440642-T-C
• chr13-94440642-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001922.5(DCT):​c.1382-566A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 145,884 control chromosomes in the GnomAD database, including 52,166 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.83 (52166 hom., cov: 24)
• Consequence: DCT NM_001922.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97

Genes affected

DCT (HGNC:2709): (dopachrome tautomerase) Predicted to enable dopachrome isomerase activity. Involved in response to blue light. Located in intracellular membrane-bounded organelle and plasma membrane. Implicated in oculocutaneous albinism. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCT	NM_001922.5	c.1382-566A>T		intron_variant		ENST00000377028.10	NP_001913.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCT	ENST00000377028.10	c.1382-566A>T		intron_variant		1	NM_001922.5	ENSP00000366227	P1
DCT	ENST00000446125.1	c.1481-566A>T		intron_variant		1		ENSP00000392762
DCT	ENST00000483392.6	c.*257-566A>T		intron_variant, NMD_transcript_variant		5		ENSP00000431275

Frequencies

GnomAD3 genomes AF: 0.833 AC: 121462 AN: 145794 Hom.: 52127 Cov.: 24

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.855

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.821

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.833 AC: 121543 AN: 145884 Hom.: 52166 Cov.: 24 AF XY: 0.825 AC XY: 58202 AN XY: 70566

Gnomad4 AFR AF: 0.937

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.846

Gnomad4 NFE AF: 0.858

Gnomad4 OTH AF: 0.821

Alfa AF: 0.798 Hom.: 1817

Asia WGS AF: 0.532 AC: 1855 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.027
DANN	Benign	0.34

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3782974; hg19: chr13-95092896;