Variant rs4842196 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 0.612 in 152,066 control chromosomes in the GnomAD database, including 30,983 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 ( 30983 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.671

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 (NFE) allele frequency at 95% confidence interval = 0.744 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:

0.613

AC:

93087

AN:

151948

Hom.:

30995

Cov.:

show subpopulations

Gnomad AFR

AF:

0.336

Gnomad AMI

AF:

0.764

Gnomad AMR

AF:

0.634

Gnomad ASJ

AF:

0.747

Gnomad EAS

AF:

0.661

Gnomad SAS

AF:

0.524

Gnomad FIN

AF:

0.737

Gnomad MID

AF:

0.696

Gnomad NFE

AF:

0.750

Gnomad OTH

AF:

0.639

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

GnomAD4 genome

AF:

0.612

AC:

93079

AN:

152066

Hom.:

30983

Cov.:

AF XY:

0.613

AC XY:

45524

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.335

Gnomad4 AMR

AF:

0.634

Gnomad4 ASJ

AF:

0.747

Gnomad4 EAS

AF:

0.660

Gnomad4 SAS

AF:

0.523

Gnomad4 FIN

AF:

0.737

Gnomad4 NFE

AF:

0.750

Gnomad4 OTH

AF:

0.632

Alfa

AF:

0.693

Hom.:

20060

Bravo

AF:

0.598

Asia WGS

AF:

0.573

AC:

1993

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

2.1

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