Variant rs2700848 details in Genebe, Genetics Data Aggregator

Variant summary

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

The variant allele was found at a frequency of 0.405 in 151,914 control chromosomes in the GnomAD database, including 13,217 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 0.40 ( 13217 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.391

Variant links:

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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 (AFR) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.405

AC:

61407

AN:

151794

Hom.:

13181

Cov.:

show subpopulations

Gnomad AFR

AF:

0.544

Gnomad AMI

AF:

0.321

Gnomad AMR

AF:

0.396

Gnomad ASJ

AF:

0.557

Gnomad EAS

AF:

0.438

Gnomad SAS

AF:

0.373

Gnomad FIN

AF:

0.289

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.332

Gnomad OTH

AF:

0.420

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

GnomAD4 genome

AF:

0.405

AC:

61506

AN:

151914

Hom.:

13217

Cov.:

AF XY:

0.402

AC XY:

29847

AN XY:

74254

show subpopulations

Gnomad4 AFR

AF:

0.544

Gnomad4 AMR

AF:

0.397

Gnomad4 ASJ

AF:

0.557

Gnomad4 EAS

AF:

0.437

Gnomad4 SAS

AF:

0.375

Gnomad4 FIN

AF:

0.289

Gnomad4 NFE

AF:

0.332

Gnomad4 OTH

AF:

0.426

Alfa

AF:

0.219

Hom.:

466

Bravo

AF:

0.419

Asia WGS

AF:

0.442

AC:

1534

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.36

DANN

Benign

0.35

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