Variant 9-32576999-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 0.204 in 151,904 control chromosomes in the GnomAD database, including 3,346 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 0.20 ( 3346 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.305

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=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.234 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:

0.204

AC:

31036

AN:

151786

Hom.:

3345

Cov.:

show subpopulations

Gnomad AFR

AF:

0.200

Gnomad AMI

AF:

0.178

Gnomad AMR

AF:

0.176

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.00503

Gnomad SAS

AF:

0.0956

Gnomad FIN

AF:

0.216

Gnomad MID

AF:

0.205

Gnomad NFE

AF:

0.237

Gnomad OTH

AF:

0.210

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

GnomAD4 genome

AF:

0.204

AC:

31036

AN:

151904

Hom.:

3346

Cov.:

AF XY:

0.201

AC XY:

14926

AN XY:

74202

show subpopulations

Gnomad4 AFR

AF:

0.200

Gnomad4 AMR

AF:

0.176

Gnomad4 ASJ

AF:

0.154

Gnomad4 EAS

AF:

0.00504

Gnomad4 SAS

AF:

0.0959

Gnomad4 FIN

AF:

0.216

Gnomad4 NFE

AF:

0.237

Gnomad4 OTH

AF:

0.207

Alfa

AF:

0.223

Hom.:

1839

Bravo

AF:

0.200

Asia WGS

AF:

0.0540

AC:

187

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

4.0

DANN

Benign

0.39

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