rs9584234

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000377028.10(DCT):​c.1179+686G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,162 control chromosomes in the GnomAD database, including 1,643 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 0.14 ( 1643 hom., cov: 32)

Consequence

DCT
ENST00000377028.10 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.459
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DCTNM_001922.5 linkuse as main transcriptc.1179+686G>A intron_variant ENST00000377028.10 NP_001913.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DCTENST00000377028.10 linkuse as main transcriptc.1179+686G>A intron_variant 1 NM_001922.5 ENSP00000366227 P1P40126-1
DCTENST00000446125.1 linkuse as main transcriptc.1179+686G>A intron_variant 1 ENSP00000392762 P40126-2
DCTENST00000483392.6 linkuse as main transcriptc.609+686G>A intron_variant, NMD_transcript_variant 5 ENSP00000431275

Frequencies

GnomAD3 genomes
AF:
0.142
AC:
21571
AN:
152044
Hom.:
1642
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.178
Gnomad AMI
AF:
0.0286
Gnomad AMR
AF:
0.143
Gnomad ASJ
AF:
0.162
Gnomad EAS
AF:
0.111
Gnomad SAS
AF:
0.197
Gnomad FIN
AF:
0.136
Gnomad MID
AF:
0.152
Gnomad NFE
AF:
0.119
Gnomad OTH
AF:
0.152
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.142
AC:
21602
AN:
152162
Hom.:
1643
Cov.:
32
AF XY:
0.142
AC XY:
10553
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.178
Gnomad4 AMR
AF:
0.143
Gnomad4 ASJ
AF:
0.162
Gnomad4 EAS
AF:
0.111
Gnomad4 SAS
AF:
0.196
Gnomad4 FIN
AF:
0.136
Gnomad4 NFE
AF:
0.119
Gnomad4 OTH
AF:
0.152
Alfa
AF:
0.125
Hom.:
2034
Bravo
AF:
0.141
Asia WGS
AF:
0.174
AC:
605
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
4.3
DANN
Benign
0.50

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9584234; hg19: chr13-95111659; API