dbSNP rs1540979: DCT:c.*1460A>T (chr13-94438438-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.996

Publications

4 publications found

Variant links:

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)

DCT links:

ENSG00000294700 (HGNC:):

ENSG00000294700 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DCT	NM_001922.5 link	c.*1460A>T		3_prime_UTR_variant	Exon 8 of 8	ENST00000377028.10	NP_001913.2	P40126-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCT	ENST00000377028.10 link	c.*1460A>T		3_prime_UTR_variant	Exon 8 of 8	1	NM_001922.5	ENSP00000366227.4		P40126-1

Frequencies

GnomAD3 genomes

AF:

0.837

AC:

127319

AN:

152052

Hom.:

54718

Cov.:

show subpopulations

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.:

AF XY:

0.793

AC XY:

60433

AN XY:

76172

show subpopulations

African (AFR)

AF:

0.946

AC:

3213

AN:

3396

American (AMR)

AF:

0.622

AC:

4133

AN:

6640

Ashkenazi Jewish (ASJ)

AF:

0.878

AC:

2626

AN:

2990

East Asian (EAS)

AF:

0.299

AC:

1521

AN:

5086

South Asian (SAS)

AF:

0.713

AC:

18899

AN:

26488

European-Finnish (FIN)

AF:

0.865

AC:

5551

AN:

6418

Middle Eastern (MID)

AF:

0.823

AC:

1395

AN:

1696

European-Non Finnish (NFE)

AF:

0.870

AC:

67002

AN:

77034

Other (OTH)

AF:

0.812

AC:

5594

AN:

6888

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.536

Heterozygous variant carriers

929

1858

2788

3717

4646

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

290

580

870

1160

1450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.837

AC:

127426

AN:

152168

Hom.:

54770

Cov.:

AF XY:

0.830

AC XY:

61726

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.939

AC:

38996

AN:

41516

American (AMR)

AF:

0.677

AC:

10342

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.875

AC:

3039

AN:

3472

East Asian (EAS)

AF:

0.285

AC:

1469

AN:

5162

South Asian (SAS)

AF:

0.696

AC:

3350

AN:

4816

European-Finnish (FIN)

AF:

0.854

AC:

9055

AN:

10604

Middle Eastern (MID)

AF:

0.847

AC:

249

AN:

294

European-Non Finnish (NFE)

AF:

0.858

AC:

58342

AN:

67998

Other (OTH)

AF:

0.827

AC:

1748

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

936

1871

2807

3742

4678

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

866

1732

2598

3464

4330

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.76

PhyloP100

-1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over