Variant rs7857826 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 0.471 in 151,630 control chromosomes in the GnomAD database, including 17,363 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 0.47 ( 17363 hom., cov: 29)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.48

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=-0.94).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.557 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:

0.471

AC:

71402

AN:

151512

Hom.:

17360

Cov.:

show subpopulations

Gnomad AFR

AF:

0.553

Gnomad AMI

AF:

0.475

Gnomad AMR

AF:

0.567

Gnomad ASJ

AF:

0.516

Gnomad EAS

AF:

0.133

Gnomad SAS

AF:

0.436

Gnomad FIN

AF:

0.406

Gnomad MID

AF:

0.525

Gnomad NFE

AF:

0.435

Gnomad OTH

AF:

0.488

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

GnomAD4 genome

AF:

0.471

AC:

71446

AN:

151630

Hom.:

17363

Cov.:

AF XY:

0.467

AC XY:

34612

AN XY:

74116

show subpopulations

Gnomad4 AFR

AF:

0.553

Gnomad4 AMR

AF:

0.567

Gnomad4 ASJ

AF:

0.516

Gnomad4 EAS

AF:

0.134

Gnomad4 SAS

AF:

0.435

Gnomad4 FIN

AF:

0.406

Gnomad4 NFE

AF:

0.435

Gnomad4 OTH

AF:

0.485

Alfa

AF:

0.286

Hom.:

636

Bravo

AF:

0.486

Asia WGS

AF:

0.301

AC:

1048

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.16

DANN

Benign

0.70

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