Variant rs9461407 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 0.305 in 136,340 control chromosomes in the GnomAD database, including 7,540 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 0.31 ( 7540 hom., cov: 25)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.67

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.305

AC:

41618

AN:

136320

Hom.:

7532

Cov.:

show subpopulations

Gnomad AFR

AF:

0.507

Gnomad AMI

AF:

0.390

Gnomad AMR

AF:

0.264

Gnomad ASJ

AF:

0.134

Gnomad EAS

AF:

0.189

Gnomad SAS

AF:

0.246

Gnomad FIN

AF:

0.153

Gnomad MID

AF:

0.202

Gnomad NFE

AF:

0.237

Gnomad OTH

AF:

0.285

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

GnomAD4 genome

AF:

0.305

AC:

41645

AN:

136340

Hom.:

7540

Cov.:

AF XY:

0.301

AC XY:

19619

AN XY:

65106

show subpopulations

Gnomad4 AFR

AF:

0.507

Gnomad4 AMR

AF:

0.263

Gnomad4 ASJ

AF:

0.134

Gnomad4 EAS

AF:

0.189

Gnomad4 SAS

AF:

0.246

Gnomad4 FIN

AF:

0.153

Gnomad4 NFE

AF:

0.237

Gnomad4 OTH

AF:

0.283

Alfa

AF:

0.209

Hom.:

807

Bravo

AF:

0.327

Asia WGS

AF:

0.204

AC:

680

AN:

3322

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

0.0020

DANN

Benign

0.42

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