Variant rs789942 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 0.728 in 152,054 control chromosomes in the GnomAD database, including 40,613 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 0.73 ( 40613 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.360

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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 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:

0.728

AC:

110648

AN:

151936

Hom.:

40598

Cov.:

show subpopulations

Gnomad AFR

AF:

0.768

Gnomad AMI

AF:

0.740

Gnomad AMR

AF:

0.666

Gnomad ASJ

AF:

0.708

Gnomad EAS

AF:

0.670

Gnomad SAS

AF:

0.577

Gnomad FIN

AF:

0.834

Gnomad MID

AF:

0.750

Gnomad NFE

AF:

0.718

Gnomad OTH

AF:

0.720

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

GnomAD4 genome

AF:

0.728

AC:

110705

AN:

152054

Hom.:

40613

Cov.:

AF XY:

0.728

AC XY:

54076

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.768

Gnomad4 AMR

AF:

0.665

Gnomad4 ASJ

AF:

0.708

Gnomad4 EAS

AF:

0.670

Gnomad4 SAS

AF:

0.577

Gnomad4 FIN

AF:

0.834

Gnomad4 NFE

AF:

0.718

Gnomad4 OTH

AF:

0.716

Alfa

AF:

0.712

Hom.:

35877

Bravo

AF:

0.720

Asia WGS

AF:

0.584

AC:

2033

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.3

DANN

Benign

0.53

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