Variant chr11-102530902-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 0.0506 in 497,540 control chromosomes in the GnomAD database, including 775 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 0.054 ( 246 hom., cov: 32)

Exomes 𝑓: 0.049 ( 529 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06

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=-0.73).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.062 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:

0.0541

AC:

8215

AN:

151978

Hom.:

247

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0502

Gnomad AMI

AF:

0.203

Gnomad AMR

AF:

0.0365

Gnomad ASJ

AF:

0.0331

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0502

Gnomad FIN

AF:

0.0553

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0636

Gnomad OTH

AF:

0.0511

GnomAD4 exome

AF:

0.0491

AC:

16963

AN:

345446

Hom.:

529

AF XY:

0.0488

AC XY:

8891

AN XY:

182016

show subpopulations

Gnomad4 AFR exome

AF:

0.0462

Gnomad4 AMR exome

AF:

0.0296

Gnomad4 ASJ exome

AF:

0.0277

Gnomad4 EAS exome

AF:

0.000349

Gnomad4 SAS exome

AF:

0.0458

Gnomad4 FIN exome

AF:

0.0552

Gnomad4 NFE exome

AF:

0.0568

Gnomad4 OTH exome

AF:

0.0469

GnomAD4 genome

AF:

0.0541

AC:

8221

AN:

152094

Hom.:

246

Cov.:

AF XY:

0.0538

AC XY:

3998

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.0503

Gnomad4 AMR

AF:

0.0364

Gnomad4 ASJ

AF:

0.0331

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.0500

Gnomad4 FIN

AF:

0.0553

Gnomad4 NFE

AF:

0.0636

Gnomad4 OTH

AF:

0.0501

Alfa

AF:

0.0561

Hom.:

Bravo

AF:

0.0527

Asia WGS

AF:

0.0210

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

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