rs11551042

chr13-94437481-T-C

Variant summary

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

The NM_001922.5(DCT):c.*2417A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,186 control chromosomes in the GnomAD database, including 2,327 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 0.16 (2327 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: DCT NM_001922.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCT	NM_001922.5	c.*2417A>G		3_prime_UTR_variant	8/8	ENST00000377028.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCT	ENST00000377028.10	c.*2417A>G		3_prime_UTR_variant	8/8	1	NM_001922.5	P1

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24075 AN: 152068 Hom.: 2324 Cov.: 33

Gnomad AFR AF: 0.0733

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.00750

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.148

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.158 AC: 24084 AN: 152186 Hom.: 2327 Cov.: 33 AF XY: 0.158 AC XY: 11751 AN XY: 74396

Gnomad4 AFR AF: 0.0734

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.00752

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.146

Alfa AF: 0.194 Hom.: 421

Bravo AF: 0.144

Asia WGS AF: 0.0680 AC: 236 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.31
Dann	Benign	0.84

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: rs11551042; hg19: chr13-95089735;