rs6492706

Variant names:

• chr13-94487130-A-G
• rs6492706
• NM_001322186.2:c.106+17781T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001322186.2(DCT):​c.106+17781T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 152,106 control chromosomes in the GnomAD database, including 35,439 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 0.68 (35439 hom., cov: 32)
• Consequence: DCT NM_001322186.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• Publications: 4 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)

ENSG00000289878 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001322186.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCT	NM_001322186.2		c.106+17781T>C		intron	N/A	NP_001309115.1
	DCT	NM_001322182.2		c.-338-20472T>C		intron	N/A	NP_001309111.1
	DCT	NM_001322183.2		c.-339+2247T>C		intron	N/A	NP_001309112.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289878	ENST00000718635.1		n.1038+2247T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102667 AN: 151988 Hom.: 35411 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.675 AC: 102740 AN: 152106 Hom.: 35439 Cov.: 32 AF XY: 0.672 AC XY: 49926 AN XY: 74348

African (AFR) AF: 0.654 AC: 27144 AN: 41480

American (AMR) AF: 0.569 AC: 8704 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2613 AN: 3466

East Asian (EAS) AF: 0.295 AC: 1526 AN: 5166

South Asian (SAS) AF: 0.616 AC: 2970 AN: 4818

European-Finnish (FIN) AF: 0.747 AC: 7904 AN: 10576

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49527 AN: 67994

Other (OTH) AF: 0.688 AC: 1452 AN: 2110

Alfa AF: 0.707 Hom.: 63912

Bravo AF: 0.654

Asia WGS AF: 0.513 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.5
DANN	Benign	0.51
PhyloP100		0.29

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6492706; hg19: chr13-95139384;