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GeneBe

rs9369240

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 0.0505 in 152,234 control chromosomes in the GnomAD database, including 280 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 0.051 ( 280 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.180
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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0607 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:
0.0506
AC:
7690
AN:
152116
Hom.:
280
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0119
Gnomad AMI
AF:
0.178
Gnomad AMR
AF:
0.0291
Gnomad ASJ
AF:
0.0899
Gnomad EAS
AF:
0.0545
Gnomad SAS
AF:
0.0226
Gnomad FIN
AF:
0.144
Gnomad MID
AF:
0.0506
Gnomad NFE
AF:
0.0622
Gnomad OTH
AF:
0.0540
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0505
AC:
7690
AN:
152234
Hom.:
280
Cov.:
32
AF XY:
0.0532
AC XY:
3957
AN XY:
74424
show subpopulations
Gnomad4 AFR
AF:
0.0119
Gnomad4 AMR
AF:
0.0290
Gnomad4 ASJ
AF:
0.0899
Gnomad4 EAS
AF:
0.0548
Gnomad4 SAS
AF:
0.0222
Gnomad4 FIN
AF:
0.144
Gnomad4 NFE
AF:
0.0622
Gnomad4 OTH
AF:
0.0549
Alfa
AF:
0.0572
Hom.:
123
Bravo
AF:
0.0424
Asia WGS
AF:
0.0350
AC:
121
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
4.0
Dann
Benign
0.86

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.

Other links and lift over

dbSNP: rs9369240; hg19: chr6-40810012; API