rs7990565

Positions:

• chr13-94460746-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-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/exons	MANE	UniProt
DCT	NM_001922.5	c.1044-520A>G		intron_variant		ENST00000377028.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCT	ENST00000377028.10	c.1044-520A>G		intron_variant		1	NM_001922.5	P1
DCT	ENST00000446125.1	c.1044-520A>G		intron_variant		1
DCT	ENST00000483392.6	c.474-520A>G		intron_variant, NMD_transcript_variant		5

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

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.454

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs7990565; hg19: chr13-95113000;