Variant rs4803413 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 0.298 in 151,874 control chromosomes in the GnomAD database, including 7,637 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 0.30 ( 7637 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.252

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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 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:

0.298

AC:

45262

AN:

151756

Hom.:

7638

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.293

Gnomad AMR

AF:

0.361

Gnomad ASJ

AF:

0.322

Gnomad EAS

AF:

0.460

Gnomad SAS

AF:

0.350

Gnomad FIN

AF:

0.435

Gnomad MID

AF:

0.385

Gnomad NFE

AF:

0.336

Gnomad OTH

AF:

0.303

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

GnomAD4 genome

AF:

0.298

AC:

45278

AN:

151874

Hom.:

7637

Cov.:

AF XY:

0.305

AC XY:

22633

AN XY:

74224

show subpopulations

Gnomad4 AFR

AF:

0.148

Gnomad4 AMR

AF:

0.362

Gnomad4 ASJ

AF:

0.322

Gnomad4 EAS

AF:

0.461

Gnomad4 SAS

AF:

0.350

Gnomad4 FIN

AF:

0.435

Gnomad4 NFE

AF:

0.336

Gnomad4 OTH

AF:

0.303

Alfa

AF:

0.205

Hom.:

507

Bravo

AF:

0.288

Asia WGS

AF:

0.374

AC:

1303

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.6

DANN

Benign

0.56

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