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GeneBe

rs9321063

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 0.0695 in 152,172 control chromosomes in the GnomAD database, including 413 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 0.069 ( 413 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.456
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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0993 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:
0.0694
AC:
10548
AN:
152054
Hom.:
412
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.102
Gnomad AMI
AF:
0.00987
Gnomad AMR
AF:
0.0753
Gnomad ASJ
AF:
0.0222
Gnomad EAS
AF:
0.00737
Gnomad SAS
AF:
0.0114
Gnomad FIN
AF:
0.0753
Gnomad MID
AF:
0.0382
Gnomad NFE
AF:
0.0599
Gnomad OTH
AF:
0.0608
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0695
AC:
10569
AN:
152172
Hom.:
413
Cov.:
33
AF XY:
0.0705
AC XY:
5243
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.102
Gnomad4 AMR
AF:
0.0752
Gnomad4 ASJ
AF:
0.0222
Gnomad4 EAS
AF:
0.00719
Gnomad4 SAS
AF:
0.0112
Gnomad4 FIN
AF:
0.0753
Gnomad4 NFE
AF:
0.0599
Gnomad4 OTH
AF:
0.0601
Alfa
AF:
0.0586
Hom.:
366
Bravo
AF:
0.0717
Asia WGS
AF:
0.0390
AC:
136
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
Cadd
Benign
0.62
Dann
Benign
0.17

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: rs9321063; hg19: chr6-98896667; API