Variant rs34809169 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 0.146 in 152,286 control chromosomes in the GnomAD database, including 1,881 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 0.15 ( 1881 hom., cov: 35)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.553

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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 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:

0.146

AC:

22211

AN:

152168

Hom.:

1872

Cov.:

show subpopulations

Gnomad AFR

AF:

0.233

Gnomad AMI

AF:

0.0757

Gnomad AMR

AF:

0.107

Gnomad ASJ

AF:

0.120

Gnomad EAS

AF:

0.0867

Gnomad SAS

AF:

0.0857

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.119

Gnomad OTH

AF:

0.150

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

GnomAD4 genome

AF:

0.146

AC:

22245

AN:

152286

Hom.:

1881

Cov.:

AF XY:

0.142

AC XY:

10544

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.233

Gnomad4 AMR

AF:

0.107

Gnomad4 ASJ

AF:

0.120

Gnomad4 EAS

AF:

0.0867

Gnomad4 SAS

AF:

0.0862

Gnomad4 FIN

AF:

0.101

Gnomad4 NFE

AF:

0.119

Gnomad4 OTH

AF:

0.151

Alfa

AF:

0.0637

Hom.:

Bravo

AF:

0.151

Asia WGS

AF:

0.112

AC:

389

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.3

DANN

Benign

0.84

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