rs2892680

Positions:

• chr13-94443275-A-G
• chr13-94443275-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000377028.10(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 ENST00000377028.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888

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=-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/exons	MANE	Protein	UniProt
DCT	NM_001922.5	c.1381+161T>C		intron_variant		ENST00000377028.10	NP_001913.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCT	ENST00000377028.10	c.1381+161T>C		intron_variant		1	NM_001922.5	ENSP00000366227	P1
DCT	ENST00000446125.1	c.1480+161T>C		intron_variant		1		ENSP00000392762
DCT	ENST00000483392.6	c.*256+161T>C		intron_variant, NMD_transcript_variant		5		ENSP00000431275

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

Gnomad4 AFR AF: 0.925

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.783

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs2892680; hg19: chr13-95095529;