Variant rs7840855 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 0.347 in 152,094 control chromosomes in the GnomAD database, including 11,378 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 0.35 ( 11378 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0260

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=-0.75).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.466 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:

0.347

AC:

52712

AN:

151978

Hom.:

11370

Cov.:

show subpopulations

Gnomad AFR

AF:

0.114

Gnomad AMI

AF:

0.363

Gnomad AMR

AF:

0.328

Gnomad ASJ

AF:

0.286

Gnomad EAS

AF:

0.182

Gnomad SAS

AF:

0.413

Gnomad FIN

AF:

0.565

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.471

Gnomad OTH

AF:

0.334

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

GnomAD4 genome

AF:

0.347

AC:

52731

AN:

152094

Hom.:

11378

Cov.:

AF XY:

0.352

AC XY:

26172

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.114

Gnomad4 AMR

AF:

0.327

Gnomad4 ASJ

AF:

0.286

Gnomad4 EAS

AF:

0.181

Gnomad4 SAS

AF:

0.416

Gnomad4 FIN

AF:

0.565

Gnomad4 NFE

AF:

0.471

Gnomad4 OTH

AF:

0.339

Alfa

AF:

0.429

Hom.:

14428

Bravo

AF:

0.316

Asia WGS

AF:

0.309

AC:

1073

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

6.1

DANN

Benign

0.66

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