Variant rs2014343 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 0.304 in 152,058 control chromosomes in the GnomAD database, including 7,485 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 0.30 ( 7485 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.283

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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 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:

0.304

AC:

46156

AN:

151940

Hom.:

7484

Cov.:

show subpopulations

Gnomad AFR

AF:

0.219

Gnomad AMI

AF:

0.359

Gnomad AMR

AF:

0.345

Gnomad ASJ

AF:

0.382

Gnomad EAS

AF:

0.435

Gnomad SAS

AF:

0.491

Gnomad FIN

AF:

0.381

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.305

Gnomad OTH

AF:

0.316

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

GnomAD4 genome

AF:

0.304

AC:

46165

AN:

152058

Hom.:

7485

Cov.:

AF XY:

0.312

AC XY:

23212

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.219

Gnomad4 AMR

AF:

0.345

Gnomad4 ASJ

AF:

0.382

Gnomad4 EAS

AF:

0.434

Gnomad4 SAS

AF:

0.492

Gnomad4 FIN

AF:

0.381

Gnomad4 NFE

AF:

0.305

Gnomad4 OTH

AF:

0.319

Alfa

AF:

0.163

Hom.:

342

Bravo

AF:

0.296

Asia WGS

AF:

0.441

AC:

1534

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.4

DANN

Benign

0.72

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