Genetic Variant NM_001922.5:c.1180-122A>C (chr13-94443759-T-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001922.5(DCT):c.1180-122A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000021 in 572,412 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)

Exomes 𝑓: 0.000021 ( 0 hom. )

Consequence

DCT
NM_001922.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.633

Publications

0 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: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCT	NM_001922.5 link	c.1180-122A>C		intron_variant	Intron 6 of 7	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.1180-122A>C		intron_variant	Intron 6 of 7	1	NM_001922.5	ENSP00000366227.4		P40126-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.0000210

AC:

AN:

572412

Hom.:

AF XY:

0.0000199

AC XY:

AN XY:

301154

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

15620

American (AMR)

AF:

0.00

AC:

AN:

29548

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

16522

East Asian (EAS)

AF:

0.00

AC:

AN:

31922

South Asian (SAS)

AF:

0.00

AC:

AN:

53500

European-Finnish (FIN)

AF:

0.00

AC:

AN:

31868

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2330

European-Non Finnish (NFE)

AF:

0.0000333

AC:

AN:

360576

Other (OTH)

AF:

0.00

AC:

AN:

30526

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.529

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

3.5

(source)

DANN

Benign

0.35

PhyloP100

0.63

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over