chr13-94458290-C-T

Variant names:

• chr13-94458290-C-T
• rs9584233
• NM_001922.5:c.1179+1801G>A

Variant summary

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

The NM_001922.5(DCT):​c.1179+1801G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,000 control chromosomes in the GnomAD database, including 1,691 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 0.14 (1691 hom., cov: 31)
• Consequence: DCT NM_001922.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCT	NM_001922.5	c.1179+1801G>A		intron_variant	Intron 6 of 7	ENST00000377028.10	NP_001913.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCT	ENST00000377028.10	c.1179+1801G>A		intron_variant	Intron 6 of 7	1	NM_001922.5	ENSP00000366227.4
DCT	ENST00000446125.1	c.1179+1801G>A		intron_variant	Intron 6 of 9	1		ENSP00000392762.1
DCT	ENST00000483392.6	n.609+1801G>A		intron_variant	Intron 5 of 8	5		ENSP00000431275.2

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21858 AN: 151882 Hom.: 1690 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.144 AC: 21888 AN: 152000 Hom.: 1691 Cov.: 31 AF XY: 0.144 AC XY: 10680 AN XY: 74310

African (AFR) AF: 0.186 AC: 7702 AN: 41436

American (AMR) AF: 0.143 AC: 2179 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 561 AN: 3470

East Asian (EAS) AF: 0.110 AC: 568 AN: 5152

South Asian (SAS) AF: 0.196 AC: 942 AN: 4814

European-Finnish (FIN) AF: 0.136 AC: 1438 AN: 10580

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8103 AN: 67980

Other (OTH) AF: 0.153 AC: 323 AN: 2106

Alfa AF: 0.127 Hom.: 939

Bravo AF: 0.143

Asia WGS AF: 0.174 AC: 604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.67
PhyloP100		-0.18
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: rs9584233; hg19: chr13-95110544;