Variant chr9-90124949-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 0.175 in 152,172 control chromosomes in the GnomAD database, including 2,440 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 0.18 ( 2440 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.520

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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 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:

0.175

AC:

26603

AN:

152054

Hom.:

2432

Cov.:

show subpopulations

Gnomad AFR

AF:

0.206

Gnomad AMI

AF:

0.138

Gnomad AMR

AF:

0.160

Gnomad ASJ

AF:

0.266

Gnomad EAS

AF:

0.143

Gnomad SAS

AF:

0.169

Gnomad FIN

AF:

0.154

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.161

Gnomad OTH

AF:

0.174

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

GnomAD4 genome

AF:

0.175

AC:

26641

AN:

152172

Hom.:

2440

Cov.:

AF XY:

0.173

AC XY:

12866

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.206

Gnomad4 AMR

AF:

0.160

Gnomad4 ASJ

AF:

0.266

Gnomad4 EAS

AF:

0.143

Gnomad4 SAS

AF:

0.169

Gnomad4 FIN

AF:

0.154

Gnomad4 NFE

AF:

0.161

Gnomad4 OTH

AF:

0.180

Alfa

AF:

0.167

Hom.:

4915

Bravo

AF:

0.177

Asia WGS

AF:

0.174

AC:

606

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.1

DANN

Benign

0.48

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