rs7990565

Variant names:

• chr13-94460746-T-C
• rs7990565
• NM_001922.5:c.1044-520A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001922.5(DCT):​c.1044-520A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,782 control chromosomes in the GnomAD database, including 20,856 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 0.50 (20856 hom., cov: 30)
• Consequence: DCT NM_001922.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.88
• Publications: 2 publications found

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]

DCT Gene-Disease associations (from GenCC):

• oculocutaneous albinism type 8

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCT	NM_001922.5	c.1044-520A>G		intron_variant	Intron 5 of 7	ENST00000377028.10	NP_001913.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCT	ENST00000377028.10	c.1044-520A>G		intron_variant	Intron 5 of 7	1	NM_001922.5	ENSP00000366227.4
DCT	ENST00000446125.1	c.1044-520A>G		intron_variant	Intron 5 of 9	1		ENSP00000392762.1
DCT	ENST00000483392.6	n.474-520A>G		intron_variant	Intron 4 of 8	5		ENSP00000431275.2

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76225 AN: 151666 Hom.: 20811 Cov.: 30

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.503 AC: 76326 AN: 151782 Hom.: 20856 Cov.: 30 AF XY: 0.496 AC XY: 36790 AN XY: 74106

African (AFR) AF: 0.709 AC: 29355 AN: 41418

American (AMR) AF: 0.389 AC: 5923 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1437 AN: 3470

East Asian (EAS) AF: 0.119 AC: 612 AN: 5156

South Asian (SAS) AF: 0.357 AC: 1709 AN: 4792

European-Finnish (FIN) AF: 0.454 AC: 4755 AN: 10478

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31083 AN: 67936

Other (OTH) AF: 0.454 AC: 956 AN: 2106

Alfa AF: 0.493 Hom.: 2394

Bravo AF: 0.500

Asia WGS AF: 0.280 AC: 973 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.54
PhyloP100		-2.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7990565; hg19: chr13-95113000;