Variant chr9-110837834-C-G 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 0.272 in 152,028 control chromosomes in the GnomAD database, including 5,823 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 0.27 ( 5823 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.650

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 (AFR) allele frequency at 95% confidence interval = 0.311 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:

0.272

AC:

41282

AN:

151910

Hom.:

5812

Cov.:

show subpopulations

Gnomad AFR

AF:

0.316

Gnomad AMI

AF:

0.200

Gnomad AMR

AF:

0.315

Gnomad ASJ

AF:

0.331

Gnomad EAS

AF:

0.277

Gnomad SAS

AF:

0.259

Gnomad FIN

AF:

0.198

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.245

Gnomad OTH

AF:

0.288

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

GnomAD4 genome

AF:

0.272

AC:

41337

AN:

152028

Hom.:

5823

Cov.:

AF XY:

0.269

AC XY:

19955

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.316

Gnomad4 AMR

AF:

0.315

Gnomad4 ASJ

AF:

0.331

Gnomad4 EAS

AF:

0.278

Gnomad4 SAS

AF:

0.260

Gnomad4 FIN

AF:

0.198

Gnomad4 NFE

AF:

0.245

Gnomad4 OTH

AF:

0.291

Alfa

AF:

0.261

Hom.:

653

Bravo

AF:

0.289

Asia WGS

AF:

0.268

AC:

931

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

0.56

DANN

Benign

0.74

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