rs11551042

Variant names:

• chr13-94437481-T-C
• rs11551042
• NM_001922.5:c.*2417A>G

Variant summary

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

The NM_001129889.3(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_001129889.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 0 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)

ENSG00000294700 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001129889.3. 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.*2417A>G		3_prime_UTR	Exon 8 of 8	NP_001913.2
	DCT	NM_001129889.3		c.*2417A>G		3_prime_UTR	Exon 10 of 10	NP_001123361.1
	DCT	NM_001322186.2		c.*2417A>G		3_prime_UTR	Exon 10 of 10	NP_001309115.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCT	ENST00000377028.10	TSL:1 MANE Select	c.*2417A>G		3_prime_UTR	Exon 8 of 8	ENSP00000366227.4
	ENSG00000294700	ENST00000725275.1		n.303+3823T>C		intron	N/A
	ENSG00000294700	ENST00000725276.1		n.241+3823T>C		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0734 AC: 3048 AN: 41544

American (AMR) AF: 0.126 AC: 1932 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 567 AN: 3468

East Asian (EAS) AF: 0.00752 AC: 39 AN: 5188

South Asian (SAS) AF: 0.123 AC: 595 AN: 4824

European-Finnish (FIN) AF: 0.231 AC: 2447 AN: 10580

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14827 AN: 67982

Other (OTH) AF: 0.146 AC: 309 AN: 2114

Alfa AF: 0.145 Hom.: 774

Bravo AF: 0.144

Asia WGS AF: 0.0680 AC: 236 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.31
DANN	Benign	0.84
PhyloP100		-2.3
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: rs11551042; hg19: chr13-95089735;