Variant rs4700774 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 0.254 in 151,986 control chromosomes in the GnomAD database, including 5,312 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 0.25 ( 5312 hom., cov: 32)

Exomes 𝑓: 0.25 ( 0 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.200

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=-1.0).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.3 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:

0.254

AC:

38594

AN:

151864

Hom.:

5303

Cov.:

show subpopulations

Gnomad AFR

AF:

0.164

Gnomad AMI

AF:

0.368

Gnomad AMR

AF:

0.307

Gnomad ASJ

AF:

0.168

Gnomad EAS

AF:

0.259

Gnomad SAS

AF:

0.108

Gnomad FIN

AF:

0.335

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.298

Gnomad OTH

AF:

0.243

GnomAD4 exome

AF:

0.250

AC:

AN:

Hom.:

AF XY:

0.00

AC XY:

AN XY:

show subpopulations

Gnomad4 NFE exome

AF:

0.500

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.254

AC:

38613

AN:

151982

Hom.:

5312

Cov.:

AF XY:

0.254

AC XY:

18894

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.163

Gnomad4 AMR

AF:

0.308

Gnomad4 ASJ

AF:

0.168

Gnomad4 EAS

AF:

0.260

Gnomad4 SAS

AF:

0.107

Gnomad4 FIN

AF:

0.335

Gnomad4 NFE

AF:

0.298

Gnomad4 OTH

AF:

0.241

Alfa

AF:

0.268

Hom.:

1060

Bravo

AF:

0.248

Asia WGS

AF:

0.184

AC:

642

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

3.3

DANN

Benign

0.44

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