rs9524491

chr13-94443137-A-T

Variant summary

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

The NM_001922.5(DCT):c.1381+299T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 152,174 control chromosomes in the GnomAD database, including 50,341 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 (50341 hom., cov: 32)
• Consequence: DCT NM_001922.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCT	NM_001922.5	c.1381+299T>A		intron_variant		ENST00000377028.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCT	ENST00000377028.10	c.1381+299T>A		intron_variant		1	NM_001922.5	P1
DCT	ENST00000446125.1	c.1480+299T>A		intron_variant		1
DCT	ENST00000483392.6	c.*256+299T>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121865 AN: 152056 Hom.: 50286 Cov.: 32

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.802 AC: 121974 AN: 152174 Hom.: 50341 Cov.: 32 AF XY: 0.792 AC XY: 58942 AN XY: 74400

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.783

Alfa AF: 0.817 Hom.: 6382

Bravo AF: 0.790

Asia WGS AF: 0.510 AC: 1777 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.46
Dann	Benign	0.48

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: rs9524491; hg19: chr13-95095391;