rs7280997

chr21-36286211-C-T

Variant summary

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

The NM_001320714.2(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_001320714.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DOP1B	NM_001320714.2	c.6161-1803C>T		intron_variant		ENST00000691173.1
DOP1B	NM_005128.4	c.6161-1803C>T		intron_variant
DOP1B	XM_017028509.2	c.5507-1803C>T		intron_variant
DOP1B	XR_937581.4	n.6307-1873C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DOP1B	ENST00000691173.1	c.6161-1803C>T		intron_variant			NM_001320714.2	P1
DOP1B	ENST00000399151.3	c.6161-1803C>T		intron_variant		1		P1
DOP1B	ENST00000685394.1	c.*652-1803C>T		intron_variant, NMD_transcript_variant
DOP1B	ENST00000693273.1	c.*4929-1803C>T		intron_variant, NMD_transcript_variant

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

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.451

Alfa AF: 0.418 Hom.: 2263

Bravo AF: 0.414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.8
Dann	Benign	0.77

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: rs7280997; hg19: chr21-37658509;