Variant rs11061209 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 0.304 in 151,988 control chromosomes in the GnomAD database, including 7,254 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 ( 7254 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.367

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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.332 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:

0.305

AC:

46260

AN:

151870

Hom.:

7249

Cov.:

show subpopulations

Gnomad AFR

AF:

0.239

Gnomad AMI

AF:

0.327

Gnomad AMR

AF:

0.314

Gnomad ASJ

AF:

0.330

Gnomad EAS

AF:

0.213

Gnomad SAS

AF:

0.219

Gnomad FIN

AF:

0.425

Gnomad MID

AF:

0.274

Gnomad NFE

AF:

0.336

Gnomad OTH

AF:

0.292

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

GnomAD4 genome

AF:

0.304

AC:

46276

AN:

151988

Hom.:

7254

Cov.:

AF XY:

0.306

AC XY:

22729

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.239

Gnomad4 AMR

AF:

0.313

Gnomad4 ASJ

AF:

0.330

Gnomad4 EAS

AF:

0.213

Gnomad4 SAS

AF:

0.219

Gnomad4 FIN

AF:

0.425

Gnomad4 NFE

AF:

0.336

Gnomad4 OTH

AF:

0.291

Alfa

AF:

0.320

Hom.:

16479

Bravo

AF:

0.293

Asia WGS

AF:

0.202

AC:

702

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.2

DANN

Benign

0.55

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