Variant 9-133532073-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 0.122 in 152,418 control chromosomes in the GnomAD database, including 1,343 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 0.12 ( 1340 hom., cov: 33)

Exomes 𝑓: 0.20 ( 3 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.590

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=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.172 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:

0.122

AC:

18543

AN:

152174

Hom.:

1338

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0578

Gnomad AMI

AF:

0.228

Gnomad AMR

AF:

0.0909

Gnomad ASJ

AF:

0.194

Gnomad EAS

AF:

0.166

Gnomad SAS

AF:

0.182

Gnomad FIN

AF:

0.133

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.153

Gnomad OTH

AF:

0.126

GnomAD4 exome

AF:

0.202

AC:

AN:

124

Hom.:

AF XY:

0.192

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0714

Gnomad4 NFE exome

AF:

0.309

Gnomad4 OTH exome

AF:

0.0625

GnomAD4 genome

AF:

0.122

AC:

18555

AN:

152294

Hom.:

1340

Cov.:

AF XY:

0.122

AC XY:

9099

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.0578

Gnomad4 AMR

AF:

0.0909

Gnomad4 ASJ

AF:

0.194

Gnomad4 EAS

AF:

0.166

Gnomad4 SAS

AF:

0.182

Gnomad4 FIN

AF:

0.133

Gnomad4 NFE

AF:

0.153

Gnomad4 OTH

AF:

0.130

Alfa

AF:

0.134

Hom.:

784

Bravo

AF:

0.112

Asia WGS

AF:

0.156

AC:

542

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.0

DANN

Benign

0.62

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