Variant rs214836 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 0.686 in 151,896 control chromosomes in the GnomAD database, including 37,056 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 0.69 ( 37056 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.897

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=-1.02).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 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:

0.686

AC:

104166

AN:

151778

Hom.:

37014

Cov.:

show subpopulations

Gnomad AFR

AF:

0.865

Gnomad AMI

AF:

0.437

Gnomad AMR

AF:

0.642

Gnomad ASJ

AF:

0.485

Gnomad EAS

AF:

0.905

Gnomad SAS

AF:

0.739

Gnomad FIN

AF:

0.640

Gnomad MID

AF:

0.592

Gnomad NFE

AF:

0.589

Gnomad OTH

AF:

0.675

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

GnomAD4 genome

AF:

0.686

AC:

104263

AN:

151896

Hom.:

37056

Cov.:

AF XY:

0.689

AC XY:

51111

AN XY:

74216

show subpopulations

Gnomad4 AFR

AF:

0.864

Gnomad4 AMR

AF:

0.642

Gnomad4 ASJ

AF:

0.485

Gnomad4 EAS

AF:

0.904

Gnomad4 SAS

AF:

0.739

Gnomad4 FIN

AF:

0.640

Gnomad4 NFE

AF:

0.589

Gnomad4 OTH

AF:

0.676

Alfa

AF:

0.654

Hom.:

4161

Bravo

AF:

0.696

Asia WGS

AF:

0.790

AC:

2744

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.84

DANN

Benign

0.19

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