Variant 11-95428411-G-A 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 0.33 in 152,012 control chromosomes in the GnomAD database, including 8,697 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 0.33 ( 8697 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0410

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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 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:

0.330

AC:

50109

AN:

151894

Hom.:

8691

Cov.:

show subpopulations

Gnomad AFR

AF:

0.416

Gnomad AMI

AF:

0.402

Gnomad AMR

AF:

0.337

Gnomad ASJ

AF:

0.358

Gnomad EAS

AF:

0.473

Gnomad SAS

AF:

0.299

Gnomad FIN

AF:

0.239

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.326

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

GnomAD4 genome

AF:

0.330

AC:

50151

AN:

152012

Hom.:

8697

Cov.:

AF XY:

0.330

AC XY:

24552

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.416

Gnomad4 AMR

AF:

0.337

Gnomad4 ASJ

AF:

0.358

Gnomad4 EAS

AF:

0.473

Gnomad4 SAS

AF:

0.297

Gnomad4 FIN

AF:

0.239

Gnomad4 NFE

AF:

0.280

Gnomad4 OTH

AF:

0.324

Alfa

AF:

0.283

Hom.:

8414

Bravo

AF:

0.343

Asia WGS

AF:

0.336

AC:

1169

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.8

DANN

Benign

0.75

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