rs7280997

Variant names:

• chr21-36286211-C-T
• rs7280997
• NM_001320714.2:c.6161-1803C>T

Variant summary

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

The NM_005128.4(DOP1B):​c.6161-1803C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,594 control chromosomes in the GnomAD database, including 13,102 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 0.41 (13102 hom., cov: 30)
• Consequence: DOP1B NM_005128.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.419 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.6161-1803C>T		intron	N/A	NP_001307643.1
	DOP1B	NM_005128.4		c.6161-1803C>T		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.6161-1803C>T		intron	N/A	ENSP00000509598.1
	DOP1B	ENST00000399151.3	TSL:1	c.6161-1803C>T		intron	N/A	ENSP00000382104.3
	DOP1B	ENST00000943076.1		c.6038-1803C>T		intron	N/A	ENSP00000613135.1

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62788 AN: 151476 Hom.: 13086 Cov.: 30

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.415 AC: 62841 AN: 151594 Hom.: 13102 Cov.: 30 AF XY: 0.412 AC XY: 30484 AN XY: 74032

African (AFR) AF: 0.405 AC: 16760 AN: 41342

American (AMR) AF: 0.415 AC: 6308 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1509 AN: 3466

East Asian (EAS) AF: 0.406 AC: 2092 AN: 5152

South Asian (SAS) AF: 0.332 AC: 1591 AN: 4792

European-Finnish (FIN) AF: 0.421 AC: 4411 AN: 10480

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28731 AN: 67874

Other (OTH) AF: 0.451 AC: 947 AN: 2102

Alfa AF: 0.418 Hom.: 2263

Bravo AF: 0.414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.77
PhyloP100		-0.45
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: rs7280997; hg19: chr21-37658509;