Variant rs3756009 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 0.32 in 152,046 control chromosomes in the GnomAD database, including 8,654 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 0.32 ( 8654 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.264

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=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 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:

0.320

AC:

48610

AN:

151928

Hom.:

8643

Cov.:

show subpopulations

Gnomad AFR

AF:

0.152

Gnomad AMI

AF:

0.486

Gnomad AMR

AF:

0.356

Gnomad ASJ

AF:

0.364

Gnomad EAS

AF:

0.330

Gnomad SAS

AF:

0.295

Gnomad FIN

AF:

0.416

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.395

Gnomad OTH

AF:

0.354

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

GnomAD4 genome

AF:

0.320

AC:

48634

AN:

152046

Hom.:

8654

Cov.:

AF XY:

0.320

AC XY:

23754

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.152

Gnomad4 AMR

AF:

0.356

Gnomad4 ASJ

AF:

0.364

Gnomad4 EAS

AF:

0.330

Gnomad4 SAS

AF:

0.295

Gnomad4 FIN

AF:

0.416

Gnomad4 NFE

AF:

0.395

Gnomad4 OTH

AF:

0.359

Alfa

AF:

0.374

Hom.:

10842

Bravo

AF:

0.309

Asia WGS

AF:

0.327

AC:

1138

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.74

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