13-94450792-C-T

Variant names:

• chr13-94450792-C-T
• rs3782972
• NM_001922.5:c.1180-7155G>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.1180-7155G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 152,076 control chromosomes in the GnomAD database, including 49,763 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 0.80 (49763 hom., cov: 31)
• Consequence: DCT NM_001922.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 5 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCT	NM_001922.5	c.1180-7155G>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.1180-7155G>A		intron_variant	Intron 6 of 7	1	NM_001922.5	ENSP00000366227.4
DCT	ENST00000446125.1	c.1235+1815G>A		intron_variant	Intron 7 of 9	1		ENSP00000392762.1
DCT	ENST00000483392.6	n.610-5031G>A		intron_variant	Intron 5 of 8	5		ENSP00000431275.2

Frequencies

GnomAD3 genomes AF: 0.797 AC: 121101 AN: 151958 Hom.: 49711 Cov.: 31

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.806

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.797 AC: 121207 AN: 152076 Hom.: 49763 Cov.: 31 AF XY: 0.788 AC XY: 58553 AN XY: 74332

African (AFR) AF: 0.915 AC: 37980 AN: 41518

American (AMR) AF: 0.651 AC: 9935 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2650 AN: 3470

East Asian (EAS) AF: 0.235 AC: 1215 AN: 5166

South Asian (SAS) AF: 0.644 AC: 3100 AN: 4814

European-Finnish (FIN) AF: 0.782 AC: 8263 AN: 10564

Middle Eastern (MID) AF: 0.801 AC: 234 AN: 292

European-Non Finnish (NFE) AF: 0.815 AC: 55417 AN: 67964

Other (OTH) AF: 0.779 AC: 1645 AN: 2112

Alfa AF: 0.795 Hom.: 50341

Bravo AF: 0.784

Asia WGS AF: 0.504 AC: 1755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.070
DANN	Benign	0.57
PhyloP100		-1.2
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: rs3782972; hg19: chr13-95103046;