Variant rs4783961 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 0.489 in 512,278 control chromosomes in the GnomAD database, including 62,567 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 0.47 ( 17289 hom., cov: 32)

Exomes 𝑓: 0.50 ( 45278 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.175

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=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.542 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:

0.471

AC:

71550

AN:

151934

Hom.:

17272

Cov.:

show subpopulations

Gnomad AFR

AF:

0.433

Gnomad AMI

AF:

0.561

Gnomad AMR

AF:

0.486

Gnomad ASJ

AF:

0.473

Gnomad EAS

AF:

0.238

Gnomad SAS

AF:

0.558

Gnomad FIN

AF:

0.447

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.505

Gnomad OTH

AF:

0.461

GnomAD3 exomes

AF:

0.480

AC:

104286

AN:

217272

Hom.:

25580

AF XY:

0.486

AC XY:

58359

AN XY:

120068

show subpopulations

Gnomad AFR exome

AF:

0.429

Gnomad AMR exome

AF:

0.519

Gnomad ASJ exome

AF:

0.484

Gnomad EAS exome

AF:

0.227

Gnomad SAS exome

AF:

0.552

Gnomad FIN exome

AF:

0.444

Gnomad NFE exome

AF:

0.499

Gnomad OTH exome

AF:

0.481

GnomAD4 exome

AF:

0.497

AC:

178942

AN:

360226

Hom.:

45278

Cov.:

AF XY:

0.502

AC XY:

103525

AN XY:

206362

show subpopulations

Gnomad4 AFR exome

AF:

0.424

Gnomad4 AMR exome

AF:

0.520

Gnomad4 ASJ exome

AF:

0.481

Gnomad4 EAS exome

AF:

0.231

Gnomad4 SAS exome

AF:

0.560

Gnomad4 FIN exome

AF:

0.444

Gnomad4 NFE exome

AF:

0.501

Gnomad4 OTH exome

AF:

0.481

GnomAD4 genome

AF:

0.471

AC:

71604

AN:

152052

Hom.:

17289

Cov.:

AF XY:

0.469

AC XY:

34854

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.434

Gnomad4 AMR

AF:

0.486

Gnomad4 ASJ

AF:

0.473

Gnomad4 EAS

AF:

0.238

Gnomad4 SAS

AF:

0.560

Gnomad4 FIN

AF:

0.447

Gnomad4 NFE

AF:

0.505

Gnomad4 OTH

AF:

0.459

Alfa

AF:

0.494

Hom.:

33690

Bravo

AF:

0.466

Asia WGS

AF:

0.373

AC:

1302

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.8

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