Variant chr11-103533183-C-T 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 0.472 in 152,022 control chromosomes in the GnomAD database, including 19,382 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 0.47 ( 19382 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.124

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=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.621 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:

0.472

AC:

71732

AN:

151904

Hom.:

19378

Cov.:

show subpopulations

Gnomad AFR

AF:

0.224

Gnomad AMI

AF:

0.646

Gnomad AMR

AF:

0.442

Gnomad ASJ

AF:

0.594

Gnomad EAS

AF:

0.237

Gnomad SAS

AF:

0.435

Gnomad FIN

AF:

0.567

Gnomad MID

AF:

0.599

Gnomad NFE

AF:

0.626

Gnomad OTH

AF:

0.511

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

GnomAD4 genome

AF:

0.472

AC:

71755

AN:

152022

Hom.:

19382

Cov.:

AF XY:

0.467

AC XY:

34690

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.224

Gnomad4 AMR

AF:

0.441

Gnomad4 ASJ

AF:

0.594

Gnomad4 EAS

AF:

0.237

Gnomad4 SAS

AF:

0.436

Gnomad4 FIN

AF:

0.567

Gnomad4 NFE

AF:

0.626

Gnomad4 OTH

AF:

0.509

Alfa

AF:

0.591

Hom.:

27681

Bravo

AF:

0.452

Asia WGS

AF:

0.335

AC:

1165

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.3

DANN

Benign

0.79

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