rs1540979

chr13-94438438-T-Achr13-94438438-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.*1460A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 288,804 control chromosomes in the GnomAD database, including 100,356 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 0.84 (54770 hom., cov: 32)
  • Exomes 𝑓: 0.80 (45586 hom.)
• Consequence: DCT NM_001922.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.996

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCT	NM_001922.5	c.*1460A>T		3_prime_UTR_variant	8/8	ENST00000377028.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCT	ENST00000377028.10	c.*1460A>T		3_prime_UTR_variant	8/8	1	NM_001922.5	P1

Frequencies

GnomAD3 genomes AF: 0.837 AC: 127319 AN: 152052 Hom.: 54718 Cov.: 32

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.827

GnomAD4 exome AF: 0.805 AC: 109934 AN: 136636 Hom.: 45586 Cov.: 0 AF XY: 0.793 AC XY: 60433 AN XY: 76172

Gnomad4 AFR exome AF: 0.946

Gnomad4 AMR exome AF: 0.622

Gnomad4 ASJ exome AF: 0.878

Gnomad4 EAS exome AF: 0.299

Gnomad4 SAS exome AF: 0.713

Gnomad4 FIN exome AF: 0.865

Gnomad4 NFE exome AF: 0.870

Gnomad4 OTH exome AF: 0.812

GnomAD4 genome AF: 0.837 AC: 127426 AN: 152168 Hom.: 54770 Cov.: 32 AF XY: 0.830 AC XY: 61726 AN XY: 74380

Gnomad4 AFR AF: 0.939

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.854

Gnomad4 NFE AF: 0.858

Gnomad4 OTH AF: 0.827

Alfa AF: 0.817 Hom.: 2619

Bravo AF: 0.821

Asia WGS AF: 0.550 AC: 1916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.12
Dann	Benign	0.76

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: rs1540979; hg19: chr13-95090692;