Variant rs720404 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 0.835 in 152,208 control chromosomes in the GnomAD database, including 53,817 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 0.84 ( 53817 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.721

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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 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:

0.836

AC:

127088

AN:

152090

Hom.:

53791

Cov.:

show subpopulations

Gnomad AFR

AF:

0.681

Gnomad AMI

AF:

0.865

Gnomad AMR

AF:

0.926

Gnomad ASJ

AF:

0.935

Gnomad EAS

AF:

0.938

Gnomad SAS

AF:

0.885

Gnomad FIN

AF:

0.915

Gnomad MID

AF:

0.908

Gnomad NFE

AF:

0.879

Gnomad OTH

AF:

0.862

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

GnomAD4 genome

AF:

0.835

AC:

127156

AN:

152208

Hom.:

53817

Cov.:

AF XY:

0.840

AC XY:

62486

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.681

Gnomad4 AMR

AF:

0.926

Gnomad4 ASJ

AF:

0.935

Gnomad4 EAS

AF:

0.937

Gnomad4 SAS

AF:

0.886

Gnomad4 FIN

AF:

0.915

Gnomad4 NFE

AF:

0.879

Gnomad4 OTH

AF:

0.863

Alfa

AF:

0.869

Hom.:

28665

Bravo

AF:

0.830

Asia WGS

AF:

0.908

AC:

3156

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

4.1

DANN

Benign

0.49

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