Variant rs7078615 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 0.704 in 152,154 control chromosomes in the GnomAD database, including 37,924 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 ( 37924 hom., cov: 34)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.149

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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.747 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:

0.705

AC:

107115

AN:

152036

Hom.:

37905

Cov.:

show subpopulations

Gnomad AFR

AF:

0.670

Gnomad AMI

AF:

0.638

Gnomad AMR

AF:

0.693

Gnomad ASJ

AF:

0.584

Gnomad EAS

AF:

0.676

Gnomad SAS

AF:

0.769

Gnomad FIN

AF:

0.698

Gnomad MID

AF:

0.718

Gnomad NFE

AF:

0.733

Gnomad OTH

AF:

0.721

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

GnomAD4 genome

AF:

0.704

AC:

107183

AN:

152154

Hom.:

37924

Cov.:

AF XY:

0.704

AC XY:

52352

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.669

Gnomad4 AMR

AF:

0.693

Gnomad4 ASJ

AF:

0.584

Gnomad4 EAS

AF:

0.676

Gnomad4 SAS

AF:

0.768

Gnomad4 FIN

AF:

0.698

Gnomad4 NFE

AF:

0.733

Gnomad4 OTH

AF:

0.724

Alfa

AF:

0.722

Hom.:

31324

Bravo

AF:

0.699

Asia WGS

AF:

0.717

AC:

2490

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.4

DANN

Benign

0.65

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