chr13-94457851-T-C

Position:

• chr13-94457851-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.1179+2240A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 151,910 control chromosomes in the GnomAD database, including 19,660 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 0.49 (19660 hom., cov: 31)
• Consequence: DCT NM_001922.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.650

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 = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCT	NM_001922.5	c.1179+2240A>G		intron_variant		ENST00000377028.10	NP_001913.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCT	ENST00000377028.10	c.1179+2240A>G		intron_variant		1	NM_001922.5	ENSP00000366227.4
DCT	ENST00000446125.1	c.1179+2240A>G		intron_variant		1		ENSP00000392762.1
DCT	ENST00000483392.6	n.609+2240A>G		intron_variant		5		ENSP00000431275.2

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74537 AN: 151792 Hom.: 19619 Cov.: 31

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.491 AC: 74635 AN: 151910 Hom.: 19660 Cov.: 31 AF XY: 0.485 AC XY: 36017 AN XY: 74234

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.444

Alfa AF: 0.441 Hom.: 11733

Bravo AF: 0.486

Asia WGS AF: 0.278 AC: 965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.38
DANN	Benign	0.27

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: rs9301959; hg19: chr13-95110105;