rs2182233

Positions:

• chr6-83082542-A-G
• chr6-83082542-A-T

Variant summary

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

The NM_015018.4(DOP1A):​c.-146-14189A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 152,094 control chromosomes in the GnomAD database, including 47,187 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 0.79 (47187 hom., cov: 32)
• Consequence: DOP1A NM_015018.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

Genes affected

DOP1A (HGNC:21194): (DOP1 leucine zipper like protein A) Predicted to be involved in Golgi to endosome transport and endoplasmic reticulum organization. Predicted to be located in Golgi membrane. Predicted to be active in endosome and trans-Golgi network. [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=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DOP1A	NM_015018.4	c.-146-14189A>G		intron_variant		ENST00000349129.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DOP1A	ENST00000349129.7	c.-146-14189A>G		intron_variant		1	NM_015018.4	P4
DOP1A	ENST00000237163.9	c.-146-14189A>G		intron_variant		5		A1

Frequencies

GnomAD3 genomes AF: 0.787 AC: 119566 AN: 151976 Hom.: 47144 Cov.: 32

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.793

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.787 AC: 119669 AN: 152094 Hom.: 47187 Cov.: 32 AF XY: 0.788 AC XY: 58578 AN XY: 74338

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.813

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.802

Gnomad4 SAS AF: 0.839

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.794

Alfa AF: 0.770 Hom.: 8197

Bravo AF: 0.791

Asia WGS AF: 0.836 AC: 2907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.33
DANN	Benign	0.49

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: rs2182233; hg19: chr6-83792261;