rs7280062

Variant names:

• chr21-36234372-T-C
• rs7280062
• NM_001320714.2:c.2622+1297T>C

Variant summary

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

The NM_005128.4(DOP1B):​c.2622+1297T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,952 control chromosomes in the GnomAD database, including 6,961 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 0.29 (6961 hom., cov: 31)
• Consequence: DOP1B NM_005128.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187
• Publications: 4 publications found

Genes affected

DOP1B (HGNC:1291): (DOP1 leucine zipper like protein B) Involved in cognition. Located in early endosome membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005128.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DOP1B	NM_001320714.2	MANE Select	c.2622+1297T>C		intron	N/A	NP_001307643.1
	DOP1B	NM_005128.4		c.2622+1297T>C		intron	N/A	NP_005119.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DOP1B	ENST00000691173.1	MANE Select	c.2622+1297T>C		intron	N/A	ENSP00000509598.1
	DOP1B	ENST00000399151.3	TSL:1	c.2622+1297T>C		intron	N/A	ENSP00000382104.3
	DOP1B	ENST00000943076.1		c.2622+1297T>C		intron	N/A	ENSP00000613135.1

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43782 AN: 151834 Hom.: 6944 Cov.: 31

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.289 AC: 43849 AN: 151952 Hom.: 6961 Cov.: 31 AF XY: 0.300 AC XY: 22278 AN XY: 74274

African (AFR) AF: 0.365 AC: 15139 AN: 41428

American (AMR) AF: 0.238 AC: 3641 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3464

East Asian (EAS) AF: 0.547 AC: 2828 AN: 5166

South Asian (SAS) AF: 0.390 AC: 1883 AN: 4824

European-Finnish (FIN) AF: 0.405 AC: 4266 AN: 10542

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.215 AC: 14609 AN: 67942

Other (OTH) AF: 0.260 AC: 549 AN: 2108

Alfa AF: 0.236 Hom.: 19222

Bravo AF: 0.279

Asia WGS AF: 0.435 AC: 1509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.80
PhyloP100		-0.19
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: rs7280062; hg19: chr21-37606670;