Variant rs2880072 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 0.485 in 151,860 control chromosomes in the GnomAD database, including 19,050 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 0.49 ( 19050 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.103

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 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:

0.485

AC:

73627

AN:

151740

Hom.:

19020

Cov.:

show subpopulations

Gnomad AFR

AF:

0.670

Gnomad AMI

AF:

0.298

Gnomad AMR

AF:

0.387

Gnomad ASJ

AF:

0.444

Gnomad EAS

AF:

0.528

Gnomad SAS

AF:

0.558

Gnomad FIN

AF:

0.385

Gnomad MID

AF:

0.389

Gnomad NFE

AF:

0.408

Gnomad OTH

AF:

0.457

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

GnomAD4 genome

AF:

0.485

AC:

73698

AN:

151860

Hom.:

19050

Cov.:

AF XY:

0.485

AC XY:

35980

AN XY:

74192

show subpopulations

Gnomad4 AFR

AF:

0.670

Gnomad4 AMR

AF:

0.386

Gnomad4 ASJ

AF:

0.444

Gnomad4 EAS

AF:

0.527

Gnomad4 SAS

AF:

0.556

Gnomad4 FIN

AF:

0.385

Gnomad4 NFE

AF:

0.408

Gnomad4 OTH

AF:

0.459

Alfa

AF:

0.450

Hom.:

2612

Bravo

AF:

0.488

Asia WGS

AF:

0.540

AC:

1881

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.3

DANN

Benign

0.37

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