Variant rs7006609 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 0.376 in 151,636 control chromosomes in the GnomAD database, including 10,986 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 0.38 ( 10986 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.54

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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 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:

0.376

AC:

56906

AN:

151520

Hom.:

10983

Cov.:

show subpopulations

Gnomad AFR

AF:

0.294

Gnomad AMI

AF:

0.280

Gnomad AMR

AF:

0.378

Gnomad ASJ

AF:

0.362

Gnomad EAS

AF:

0.421

Gnomad SAS

AF:

0.315

Gnomad FIN

AF:

0.471

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.413

Gnomad OTH

AF:

0.392

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

GnomAD4 genome

AF:

0.376

AC:

56941

AN:

151636

Hom.:

10986

Cov.:

AF XY:

0.377

AC XY:

27966

AN XY:

74106

show subpopulations

Gnomad4 AFR

AF:

0.294

Gnomad4 AMR

AF:

0.378

Gnomad4 ASJ

AF:

0.362

Gnomad4 EAS

AF:

0.422

Gnomad4 SAS

AF:

0.315

Gnomad4 FIN

AF:

0.471

Gnomad4 NFE

AF:

0.413

Gnomad4 OTH

AF:

0.392

Alfa

AF:

0.310

Hom.:

1231

Bravo

AF:

0.367

Asia WGS

AF:

0.382

AC:

1325

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.31

DANN

Benign

0.46

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