rs9516414

Positions:

• chr13-94443077-T-C
• chr13-94443077-T-G

Variant summary

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

The NM_001922.5(DCT):​c.1381+359A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 152,114 control chromosomes in the GnomAD database, including 45,450 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 0.76 (45450 hom., cov: 32)
• Consequence: DCT NM_001922.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCT	NM_001922.5	c.1381+359A>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.1381+359A>G		intron_variant		1	NM_001922.5	ENSP00000366227	P1
DCT	ENST00000446125.1	c.1480+359A>G		intron_variant		1		ENSP00000392762
DCT	ENST00000483392.6	c.*256+359A>G		intron_variant, NMD_transcript_variant		5		ENSP00000431275

Frequencies

GnomAD3 genomes AF: 0.764 AC: 116100 AN: 151996 Hom.: 45412 Cov.: 32

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.764 AC: 116183 AN: 152114 Hom.: 45450 Cov.: 32 AF XY: 0.755 AC XY: 56147 AN XY: 74362

Gnomad4 AFR AF: 0.795

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.759

Alfa AF: 0.795 Hom.: 6005

Bravo AF: 0.747

Asia WGS AF: 0.501 AC: 1742 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.78

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: rs9516414; hg19: chr13-95095331;