Variant rs996343 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 0.397 in 152,000 control chromosomes in the GnomAD database, including 13,010 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 0.40 ( 13010 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.583

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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 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:

0.398

AC:

60390

AN:

151882

Hom.:

13013

Cov.:

show subpopulations

Gnomad AFR

AF:

0.281

Gnomad AMI

AF:

0.369

Gnomad AMR

AF:

0.417

Gnomad ASJ

AF:

0.381

Gnomad EAS

AF:

0.787

Gnomad SAS

AF:

0.595

Gnomad FIN

AF:

0.458

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.413

Gnomad OTH

AF:

0.394

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

GnomAD4 genome

AF:

0.397

AC:

60405

AN:

152000

Hom.:

13010

Cov.:

AF XY:

0.405

AC XY:

30102

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.281

Gnomad4 AMR

AF:

0.417

Gnomad4 ASJ

AF:

0.381

Gnomad4 EAS

AF:

0.787

Gnomad4 SAS

AF:

0.595

Gnomad4 FIN

AF:

0.458

Gnomad4 NFE

AF:

0.413

Gnomad4 OTH

AF:

0.396

Alfa

AF:

0.418

Hom.:

2318

Bravo

AF:

0.390

Asia WGS

AF:

0.680

AC:

2363

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.27

DANN

Benign

0.45

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