Variant rs7970841 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 0.764 in 152,050 control chromosomes in the GnomAD database, including 44,838 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 0.76 ( 44838 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.234

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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.868 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:

0.764

AC:

116046

AN:

151932

Hom.:

44784

Cov.:

show subpopulations

Gnomad AFR

AF:

0.875

Gnomad AMI

AF:

0.780

Gnomad AMR

AF:

0.797

Gnomad ASJ

AF:

0.673

Gnomad EAS

AF:

0.844

Gnomad SAS

AF:

0.790

Gnomad FIN

AF:

0.675

Gnomad MID

AF:

0.790

Gnomad NFE

AF:

0.699

Gnomad OTH

AF:

0.767

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

GnomAD4 genome

AF:

0.764

AC:

116163

AN:

152050

Hom.:

44838

Cov.:

AF XY:

0.765

AC XY:

56794

AN XY:

74284

show subpopulations

Gnomad4 AFR

AF:

0.875

Gnomad4 AMR

AF:

0.797

Gnomad4 ASJ

AF:

0.673

Gnomad4 EAS

AF:

0.843

Gnomad4 SAS

AF:

0.789

Gnomad4 FIN

AF:

0.675

Gnomad4 NFE

AF:

0.699

Gnomad4 OTH

AF:

0.771

Alfa

AF:

0.707

Hom.:

14014

Bravo

AF:

0.780

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

4.3

DANN

Benign

0.72

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