Variant rs2502807 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 0.704 in 152,190 control chromosomes in the GnomAD database, including 38,692 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 0.70 ( 38692 hom., cov: 34)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.916

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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.704

AC:

106994

AN:

152072

Hom.:

38636

Cov.:

show subpopulations

Gnomad AFR

AF:

0.844

Gnomad AMI

AF:

0.624

Gnomad AMR

AF:

0.747

Gnomad ASJ

AF:

0.615

Gnomad EAS

AF:

0.944

Gnomad SAS

AF:

0.697

Gnomad FIN

AF:

0.630

Gnomad MID

AF:

0.630

Gnomad NFE

AF:

0.608

Gnomad OTH

AF:

0.686

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

GnomAD4 genome

AF:

0.704

AC:

107105

AN:

152190

Hom.:

38692

Cov.:

AF XY:

0.706

AC XY:

52497

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.844

Gnomad4 AMR

AF:

0.748

Gnomad4 ASJ

AF:

0.615

Gnomad4 EAS

AF:

0.943

Gnomad4 SAS

AF:

0.695

Gnomad4 FIN

AF:

0.630

Gnomad4 NFE

AF:

0.608

Gnomad4 OTH

AF:

0.690

Alfa

AF:

0.642

Hom.:

19622

Bravo

AF:

0.722

Asia WGS

AF:

0.833

AC:

2893

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

6.0

DANN

Benign

0.65

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