Variant rs78216286 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 0.0727 in 151,574 control chromosomes in the GnomAD database, including 636 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 0.073 ( 636 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.212

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=-0.81).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.133 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:

0.0725

AC:

10984

AN:

151454

Hom.:

635

Cov.:

show subpopulations

Gnomad AFR

AF:

0.128

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.138

Gnomad ASJ

AF:

0.0327

Gnomad EAS

AF:

0.117

Gnomad SAS

AF:

0.117

Gnomad FIN

AF:

0.0113

Gnomad MID

AF:

0.0318

Gnomad NFE

AF:

0.0307

Gnomad OTH

AF:

0.0639

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

GnomAD4 genome

AF:

0.0727

AC:

11019

AN:

151574

Hom.:

636

Cov.:

AF XY:

0.0748

AC XY:

5542

AN XY:

74052

show subpopulations

Gnomad4 AFR

AF:

0.128

Gnomad4 AMR

AF:

0.138

Gnomad4 ASJ

AF:

0.0327

Gnomad4 EAS

AF:

0.118

Gnomad4 SAS

AF:

0.118

Gnomad4 FIN

AF:

0.0113

Gnomad4 NFE

AF:

0.0307

Gnomad4 OTH

AF:

0.0661

Alfa

AF:

0.0521

Hom.:

Bravo

AF:

0.0849

Asia WGS

AF:

0.111

AC:

385

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

DANN

Benign

0.71

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