Variant rs4735692 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 0.484 in 151,420 control chromosomes in the GnomAD database, including 18,262 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 0.48 ( 18262 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.369

Variant links:

Genome browser will be placed here

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 (EAS) allele frequency at 95% confidence interval = 0.595 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:

0.484

AC:

73233

AN:

151302

Hom.:

18235

Cov.:

show subpopulations

Gnomad AFR

AF:

0.575

Gnomad AMI

AF:

0.489

Gnomad AMR

AF:

0.531

Gnomad ASJ

AF:

0.420

Gnomad EAS

AF:

0.613

Gnomad SAS

AF:

0.572

Gnomad FIN

AF:

0.403

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.418

Gnomad OTH

AF:

0.472

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

GnomAD4 genome

AF:

0.484

AC:

73304

AN:

151420

Hom.:

18262

Cov.:

AF XY:

0.487

AC XY:

36065

AN XY:

74024

show subpopulations

Gnomad4 AFR

AF:

0.575

Gnomad4 AMR

AF:

0.532

Gnomad4 ASJ

AF:

0.420

Gnomad4 EAS

AF:

0.612

Gnomad4 SAS

AF:

0.572

Gnomad4 FIN

AF:

0.403

Gnomad4 NFE

AF:

0.418

Gnomad4 OTH

AF:

0.473

Alfa

AF:

0.431

Hom.:

23054

Bravo

AF:

0.492

Asia WGS

AF:

0.583

AC:

2023

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.6

DANN

Benign

0.60

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