chr13-94450792-C-T

Position:

• chr13-94450792-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.94).
• 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/exons	MANE	Protein	UniProt
DCT	NM_001922.5	c.1180-7155G>A		intron_variant		ENST00000377028.10	NP_001913.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCT	ENST00000377028.10	c.1180-7155G>A		intron_variant		1	NM_001922.5	ENSP00000366227	P1
DCT	ENST00000446125.1	c.1235+1815G>A		intron_variant		1		ENSP00000392762
DCT	ENST00000483392.6	c.610-5031G>A		intron_variant, NMD_transcript_variant		5		ENSP00000431275

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

Gnomad4 AFR AF: 0.915

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.764

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.779

Alfa AF: 0.788 Hom.: 36634

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

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: rs3782972; hg19: chr13-95103046;