Variant 9-130565233-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 0.321 in 151,934 control chromosomes in the GnomAD database, including 8,165 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 0.32 ( 8165 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.438

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=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 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:

0.321

AC:

48680

AN:

151816

Hom.:

8171

Cov.:

show subpopulations

Gnomad AFR

AF:

0.225

Gnomad AMI

AF:

0.193

Gnomad AMR

AF:

0.391

Gnomad ASJ

AF:

0.318

Gnomad EAS

AF:

0.507

Gnomad SAS

AF:

0.290

Gnomad FIN

AF:

0.424

Gnomad MID

AF:

0.287

Gnomad NFE

AF:

0.336

Gnomad OTH

AF:

0.340

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

GnomAD4 genome

AF:

0.321

AC:

48695

AN:

151934

Hom.:

8165

Cov.:

AF XY:

0.327

AC XY:

24299

AN XY:

74244

show subpopulations

Gnomad4 AFR

AF:

0.225

Gnomad4 AMR

AF:

0.391

Gnomad4 ASJ

AF:

0.318

Gnomad4 EAS

AF:

0.506

Gnomad4 SAS

AF:

0.289

Gnomad4 FIN

AF:

0.424

Gnomad4 NFE

AF:

0.336

Gnomad4 OTH

AF:

0.344

Alfa

AF:

0.340

Hom.:

15646

Bravo

AF:

0.317

Asia WGS

AF:

0.392

AC:

1360

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.53

DANN

Benign

0.64

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