rs9516418

Variant names:

• chr13-94459255-T-C
• rs9516418
• NM_001922.5:c.1179+836A>G

Variant summary

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

The NM_001922.5(DCT):​c.1179+836A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,052 control chromosomes in the GnomAD database, including 10,290 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 0.36 (10290 hom., cov: 32)
• Consequence: DCT NM_001922.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• Publications: 5 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)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001922.5. 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_001922.5	MANE Select	c.1179+836A>G		intron	N/A	NP_001913.2
	DCT	NM_001129889.3		c.1179+836A>G		intron	N/A	NP_001123361.1	P40126-2
	DCT	NM_001322186.2		c.990+836A>G		intron	N/A	NP_001309115.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCT	ENST00000377028.10	TSL:1 MANE Select	c.1179+836A>G		intron	N/A	ENSP00000366227.4	P40126-1
	DCT	ENST00000446125.1	TSL:1	c.1179+836A>G		intron	N/A	ENSP00000392762.1	P40126-2
	DCT	ENST00000483392.6	TSL:5	n.609+836A>G		intron	N/A	ENSP00000431275.2	A0A0A0MTD3

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55127 AN: 151934 Hom.: 10282 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.363 AC: 55177 AN: 152052 Hom.: 10290 Cov.: 32 AF XY: 0.359 AC XY: 26706 AN XY: 74320

African (AFR) AF: 0.394 AC: 16341 AN: 41456

American (AMR) AF: 0.312 AC: 4774 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1266 AN: 3470

East Asian (EAS) AF: 0.118 AC: 612 AN: 5176

South Asian (SAS) AF: 0.342 AC: 1648 AN: 4822

European-Finnish (FIN) AF: 0.367 AC: 3873 AN: 10552

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25526 AN: 67972

Other (OTH) AF: 0.346 AC: 733 AN: 2116

Alfa AF: 0.368 Hom.: 16069

Bravo AF: 0.353

Asia WGS AF: 0.252 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.69
PhyloP100		0.063
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9516418; hg19: chr13-95111509;