Variant rs4742409 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 0.611 in 152,012 control chromosomes in the GnomAD database, including 30,004 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 0.61 ( 30004 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.476

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=-0.76).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 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:

0.611

AC:

92807

AN:

151894

Hom.:

29999

Cov.:

show subpopulations

Gnomad AFR

AF:

0.381

Gnomad AMI

AF:

0.837

Gnomad AMR

AF:

0.683

Gnomad ASJ

AF:

0.676

Gnomad EAS

AF:

0.901

Gnomad SAS

AF:

0.715

Gnomad FIN

AF:

0.661

Gnomad MID

AF:

0.646

Gnomad NFE

AF:

0.690

Gnomad OTH

AF:

0.646

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

GnomAD4 genome

AF:

0.611

AC:

92837

AN:

152012

Hom.:

30004

Cov.:

AF XY:

0.614

AC XY:

45644

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.381

Gnomad4 AMR

AF:

0.683

Gnomad4 ASJ

AF:

0.676

Gnomad4 EAS

AF:

0.902

Gnomad4 SAS

AF:

0.715

Gnomad4 FIN

AF:

0.661

Gnomad4 NFE

AF:

0.690

Gnomad4 OTH

AF:

0.644

Alfa

AF:

0.677

Hom.:

45131

Bravo

AF:

0.606

Asia WGS

AF:

0.733

AC:

2547

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

9.9

DANN

Benign

0.89

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