Variant rs61927768 details in Genebe, Genetics Data Aggregator

Variant summary

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

The 12-50504945-G-A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 533,844 control chromosomes in the GnomAD database, including 31,510 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 0.20 ( 3824 hom., cov: 32)

Exomes 𝑓: 0.30 ( 27686 hom. )

Consequence

DIP2B
NM_173602.3 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.69

Variant links:

Genes affected

DIP2B (HGNC:29284): (disco interacting protein 2 homolog B) This gene encodes a member of the disco-interacting protein homolog 2 protein family. The encoded protein contains a binding site for the transcriptional regulator DNA methyltransferase 1 associated protein 1 as well as AMP-binding sites. The presence of these sites suggests that the encoded protein may participate in DNA methylation. This gene is located near a folate-sensitive fragile site, and CGG-repeat expansion in the promoter of this gene which affects transcription has been detected in individuals containing this fragile site on chromosome 12. [provided by RefSeq, Aug 2011]

DIP2B links:

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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=-0.48).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DIP2B	NM_173602.3 linkuse as main transcript			upstream_gene_variant		ENST00000301180.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIP2B	ENST00000301180.10 linkuse as main transcript			upstream_gene_variant		5	NM_173602.3	P1
DIP2B	ENST00000549620.5 linkuse as main transcript			upstream_gene_variant		1

Frequencies

GnomAD3 genomes

AF:

0.199

AC:

29843

AN:

149824

Hom.:

3824

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0562

Gnomad AMI

AF:

0.186

Gnomad AMR

AF:

0.167

Gnomad ASJ

AF:

0.175

Gnomad EAS

AF:

0.0611

Gnomad SAS

AF:

0.241

Gnomad FIN

AF:

0.240

Gnomad MID

AF:

0.211

Gnomad NFE

AF:

0.296

Gnomad OTH

AF:

0.226

GnomAD4 exome

AF:

0.301

AC:

115416

AN:

383896

Hom.:

27686

Cov.:

AF XY:

0.300

AC XY:

62368

AN XY:

207948

show subpopulations

Gnomad4 AFR exome

AF:

0.0608

Gnomad4 AMR exome

AF:

0.174

Gnomad4 ASJ exome

AF:

0.236

Gnomad4 EAS exome

AF:

0.0692

Gnomad4 SAS exome

AF:

0.279

Gnomad4 FIN exome

AF:

0.295

Gnomad4 NFE exome

AF:

0.352

Gnomad4 OTH exome

AF:

0.292

GnomAD4 genome

AF:

0.199

AC:

29837

AN:

149948

Hom.:

3824

Cov.:

AF XY:

0.195

AC XY:

14292

AN XY:

73224

show subpopulations

Gnomad4 AFR

AF:

0.0560

Gnomad4 AMR

AF:

0.166

Gnomad4 ASJ

AF:

0.175

Gnomad4 EAS

AF:

0.0610

Gnomad4 SAS

AF:

0.242

Gnomad4 FIN

AF:

0.240

Gnomad4 NFE

AF:

0.296

Gnomad4 OTH

AF:

0.224

Alfa

AF:

0.127

Hom.:

247

Bravo

AF:

0.184

Asia WGS

AF:

0.155

AC:

538

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

DANN

Benign

0.97

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over