rs2892680

Variant names:

• chr13-94443275-A-G
• rs2892680
• NM_001922.5:c.1381+161T>C

Your query was ambiguous. Multiple possible variants found:

• chr13-94443275-A-G
• chr13-94443275-A-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.1381+161T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152,210 control chromosomes in the GnomAD database, including 50,310 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 (50310 hom., cov: 33)
• Consequence: DCT NM_001922.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888
• 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)

ENSG00000294700 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCT	NM_001922.5	c.1381+161T>C		intron_variant	Intron 7 of 7	ENST00000377028.10	NP_001913.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCT	ENST00000377028.10	c.1381+161T>C		intron_variant	Intron 7 of 7	1	NM_001922.5	ENSP00000366227.4

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121844 AN: 152092 Hom.: 50257 Cov.: 33

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.801 AC: 121951 AN: 152210 Hom.: 50310 Cov.: 33 AF XY: 0.792 AC XY: 58936 AN XY: 74424

African (AFR) AF: 0.925 AC: 38449 AN: 41550

American (AMR) AF: 0.655 AC: 10012 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2665 AN: 3470

East Asian (EAS) AF: 0.253 AC: 1307 AN: 5174

South Asian (SAS) AF: 0.643 AC: 3100 AN: 4820

European-Finnish (FIN) AF: 0.782 AC: 8281 AN: 10594

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55477 AN: 68000

Other (OTH) AF: 0.783 AC: 1655 AN: 2114

Alfa AF: 0.813 Hom.: 5940

Bravo AF: 0.789

Asia WGS AF: 0.510 AC: 1777 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.045
DANN	Benign	0.26
PhyloP100		-0.89
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: rs2892680; hg19: chr13-95095529;