Variant chr9-75700836-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 0.197 in 152,026 control chromosomes in the GnomAD database, including 3,135 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 ( 3135 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.179

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.205 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:

0.197

AC:

29991

AN:

151908

Hom.:

3133

Cov.:

show subpopulations

Gnomad AFR

AF:

0.184

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.184

Gnomad EAS

AF:

0.0624

Gnomad SAS

AF:

0.112

Gnomad FIN

AF:

0.295

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.206

Gnomad OTH

AF:

0.186

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

GnomAD4 genome

AF:

0.197

AC:

30008

AN:

152026

Hom.:

3135

Cov.:

AF XY:

0.200

AC XY:

14831

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.184

Gnomad4 AMR

AF:

0.211

Gnomad4 ASJ

AF:

0.184

Gnomad4 EAS

AF:

0.0625

Gnomad4 SAS

AF:

0.113

Gnomad4 FIN

AF:

0.295

Gnomad4 NFE

AF:

0.206

Gnomad4 OTH

AF:

0.184

Alfa

AF:

0.198

Hom.:

6312

Bravo

AF:

0.191

Asia WGS

AF:

0.0790

AC:

276

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.4

DANN

Benign

0.70

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