13-94442762-T-C

Variant summary

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

The NM_001922.5(DCT):c.1381+674A>G 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 152,186 control chromosomes in the GnomAD database, including 1,907 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 (1907 hom., cov: 32)
• Consequence: DCT NM_001922.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCT	NM_001922.5	c.1381+674A>G		intron_variant		ENST00000377028.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCT	ENST00000377028.10	c.1381+674A>G		intron_variant		1	NM_001922.5	P1
DCT	ENST00000446125.1	c.1480+674A>G		intron_variant		1
DCT	ENST00000483392.6	c.*256+674A>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21970 AN: 152068 Hom.: 1906 Cov.: 32

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.00769

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.144 AC: 21974 AN: 152186 Hom.: 1907 Cov.: 32 AF XY: 0.143 AC XY: 10663 AN XY: 74382

Gnomad4 AFR AF: 0.0695

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.00770

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.131

Alfa AF: 0.176 Hom.: 333

Bravo AF: 0.132

Asia WGS AF: 0.0570 AC: 200 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.2
Dann	Benign	0.45

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: rs16949829; hg19: chr13-95095016;