Variant rs7040848 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 0.695 in 151,994 control chromosomes in the GnomAD database, including 38,645 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 0.70 ( 38645 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.724

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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.908 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:

0.695

AC:

105571

AN:

151876

Hom.:

38578

Cov.:

show subpopulations

Gnomad AFR

AF:

0.916

Gnomad AMI

AF:

0.349

Gnomad AMR

AF:

0.683

Gnomad ASJ

AF:

0.621

Gnomad EAS

AF:

0.882

Gnomad SAS

AF:

0.707

Gnomad FIN

AF:

0.643

Gnomad MID

AF:

0.694

Gnomad NFE

AF:

0.565

Gnomad OTH

AF:

0.699

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

GnomAD4 genome

AF:

0.695

AC:

105697

AN:

151994

Hom.:

38645

Cov.:

AF XY:

0.699

AC XY:

51954

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.916

Gnomad4 AMR

AF:

0.683

Gnomad4 ASJ

AF:

0.621

Gnomad4 EAS

AF:

0.882

Gnomad4 SAS

AF:

0.707

Gnomad4 FIN

AF:

0.643

Gnomad4 NFE

AF:

0.565

Gnomad4 OTH

AF:

0.703

Alfa

AF:

0.593

Hom.:

11412

Bravo

AF:

0.711

Asia WGS

AF:

0.799

AC:

2770

AN:

3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

4.6

DANN

Benign

0.68

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