Variant 9-117700437-A-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 0.22 in 152,152 control chromosomes in the GnomAD database, including 4,102 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 0.22 ( 4102 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0710

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 (NFE) allele frequency at 95% confidence interval = 0.277 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:

0.220

AC:

33441

AN:

152034

Hom.:

4101

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.330

Gnomad AMR

AF:

0.224

Gnomad ASJ

AF:

0.242

Gnomad EAS

AF:

0.00231

Gnomad SAS

AF:

0.219

Gnomad FIN

AF:

0.232

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.281

Gnomad OTH

AF:

0.237

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

GnomAD4 genome

AF:

0.220

AC:

33449

AN:

152152

Hom.:

4102

Cov.:

AF XY:

0.217

AC XY:

16113

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.137

Gnomad4 AMR

AF:

0.224

Gnomad4 ASJ

AF:

0.242

Gnomad4 EAS

AF:

0.00251

Gnomad4 SAS

AF:

0.219

Gnomad4 FIN

AF:

0.232

Gnomad4 NFE

AF:

0.281

Gnomad4 OTH

AF:

0.235

Alfa

AF:

0.266

Hom.:

11693

Bravo

AF:

0.217

Asia WGS

AF:

0.104

AC:

364

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

6.0

DANN

Benign

0.66

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