Variant rs733164 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.3 in 152,062 control chromosomes in the GnomAD database, including 6,974 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 ( 6974 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.83

Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 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:

0.300

AC:

45592

AN:

151944

Hom.:

6973

Cov.:

show subpopulations

Gnomad AFR

AF:

0.326

Gnomad AMI

AF:

0.474

Gnomad AMR

AF:

0.306

Gnomad ASJ

AF:

0.363

Gnomad EAS

AF:

0.137

Gnomad SAS

AF:

0.244

Gnomad FIN

AF:

0.305

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.293

Gnomad OTH

AF:

0.295

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

GnomAD4 genome

AF:

0.300

AC:

45621

AN:

152062

Hom.:

6974

Cov.:

AF XY:

0.297

AC XY:

22053

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.326

Gnomad4 AMR

AF:

0.306

Gnomad4 ASJ

AF:

0.363

Gnomad4 EAS

AF:

0.137

Gnomad4 SAS

AF:

0.245

Gnomad4 FIN

AF:

0.305

Gnomad4 NFE

AF:

0.293

Gnomad4 OTH

AF:

0.296

Alfa

AF:

0.297

Hom.:

8836

Bravo

AF:

0.307

Asia WGS

AF:

0.247

AC:

861

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

DANN

Benign

0.78

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