13-94440642-T-A

Variant names:

• chr13-94440642-T-A
• rs3782974
• NM_001922.5:c.1382-566A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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)

ENSG00000294700 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001922.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCT	NM_001922.5	MANE Select	c.1382-566A>T		intron	N/A	NP_001913.2
	DCT	NM_001129889.3		c.1481-566A>T		intron	N/A	NP_001123361.1
	DCT	NM_001322186.2		c.1193-566A>T		intron	N/A	NP_001309115.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCT	ENST00000377028.10	TSL:1 MANE Select	c.1382-566A>T		intron	N/A	ENSP00000366227.4
	DCT	ENST00000446125.1	TSL:1	c.1481-566A>T		intron	N/A	ENSP00000392762.1
	DCT	ENST00000483392.6	TSL:5	n.*257-566A>T		intron	N/A	ENSP00000431275.2

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

African (AFR) AF: 0.937 AC: 36644 AN: 39112

American (AMR) AF: 0.669 AC: 9591 AN: 14346

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3026 AN: 3458

East Asian (EAS) AF: 0.241 AC: 1216 AN: 5048

South Asian (SAS) AF: 0.688 AC: 3255 AN: 4728

European-Finnish (FIN) AF: 0.846 AC: 7279 AN: 8600

Middle Eastern (MID) AF: 0.848 AC: 229 AN: 270

European-Non Finnish (NFE) AF: 0.858 AC: 57792 AN: 67372

Other (OTH) AF: 0.821 AC: 1689 AN: 2056

Alfa AF: 0.798 Hom.: 1817

Asia WGS AF: 0.532 AC: 1855 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.027
DANN	Benign	0.34
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3782974; hg19: chr13-95092896;