Variant rs11085374 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 0.352 in 151,898 control chromosomes in the GnomAD database, including 10,323 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 0.35 ( 10323 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.40

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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 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:

0.352

AC:

53451

AN:

151778

Hom.:

10297

Cov.:

show subpopulations

Gnomad AFR

AF:

0.503

Gnomad AMI

AF:

0.361

Gnomad AMR

AF:

0.240

Gnomad ASJ

AF:

0.320

Gnomad EAS

AF:

0.176

Gnomad SAS

AF:

0.251

Gnomad FIN

AF:

0.309

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.315

Gnomad OTH

AF:

0.337

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

GnomAD4 genome

AF:

0.352

AC:

53523

AN:

151898

Hom.:

10323

Cov.:

AF XY:

0.347

AC XY:

25761

AN XY:

74238

show subpopulations

Gnomad4 AFR

AF:

0.504

Gnomad4 AMR

AF:

0.239

Gnomad4 ASJ

AF:

0.320

Gnomad4 EAS

AF:

0.177

Gnomad4 SAS

AF:

0.250

Gnomad4 FIN

AF:

0.309

Gnomad4 NFE

AF:

0.315

Gnomad4 OTH

AF:

0.334

Alfa

AF:

0.197

Hom.:

395

Bravo

AF:

0.355

Asia WGS

AF:

0.248

AC:

864

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.85

DANN

Benign

0.18

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