Variant rs2275073 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 0.615 in 173,600 control chromosomes in the GnomAD database, including 37,947 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 0.60 ( 32068 hom., cov: 31)

Exomes 𝑓: 0.71 ( 5879 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.373

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=-0.78).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 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:

0.603

AC:

91531

AN:

151892

Hom.:

32070

Cov.:

show subpopulations

Gnomad AFR

AF:

0.262

Gnomad AMI

AF:

0.898

Gnomad AMR

AF:

0.705

Gnomad ASJ

AF:

0.743

Gnomad EAS

AF:

0.145

Gnomad SAS

AF:

0.614

Gnomad FIN

AF:

0.755

Gnomad MID

AF:

0.769

Gnomad NFE

AF:

0.784

Gnomad OTH

AF:

0.654

GnomAD4 exome

AF:

0.707

AC:

15262

AN:

21588

Hom.:

5879

AF XY:

0.703

AC XY:

8081

AN XY:

11488

show subpopulations

Gnomad4 AFR exome

AF:

0.259

Gnomad4 AMR exome

AF:

0.735

Gnomad4 ASJ exome

AF:

0.740

Gnomad4 EAS exome

AF:

0.172

Gnomad4 SAS exome

AF:

0.633

Gnomad4 FIN exome

AF:

0.736

Gnomad4 NFE exome

AF:

0.781

Gnomad4 OTH exome

AF:

0.726

GnomAD4 genome

AF:

0.602

AC:

91522

AN:

152012

Hom.:

32068

Cov.:

AF XY:

0.601

AC XY:

44651

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.261

Gnomad4 AMR

AF:

0.705

Gnomad4 ASJ

AF:

0.743

Gnomad4 EAS

AF:

0.145

Gnomad4 SAS

AF:

0.613

Gnomad4 FIN

AF:

0.755

Gnomad4 NFE

AF:

0.784

Gnomad4 OTH

AF:

0.652

Alfa

AF:

0.714

Hom.:

13463

Bravo

AF:

0.584

Asia WGS

AF:

0.398

AC:

1386

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.52

DANN

Benign

0.82

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