rs9275535

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 0.589 in 151,764 control chromosomes in the GnomAD database, including 26,733 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 0.59 ( 26733 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.38
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=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.590
AC:
89402
AN:
151646
Hom.:
26726
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.561
Gnomad AMI
AF:
0.728
Gnomad AMR
AF:
0.643
Gnomad ASJ
AF:
0.753
Gnomad EAS
AF:
0.731
Gnomad SAS
AF:
0.668
Gnomad FIN
AF:
0.543
Gnomad MID
AF:
0.684
Gnomad NFE
AF:
0.574
Gnomad OTH
AF:
0.638
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.589
AC:
89457
AN:
151764
Hom.:
26733
Cov.:
31
AF XY:
0.590
AC XY:
43738
AN XY:
74160
show subpopulations
Gnomad4 AFR
AF:
0.561
Gnomad4 AMR
AF:
0.643
Gnomad4 ASJ
AF:
0.753
Gnomad4 EAS
AF:
0.730
Gnomad4 SAS
AF:
0.667
Gnomad4 FIN
AF:
0.543
Gnomad4 NFE
AF:
0.574
Gnomad4 OTH
AF:
0.640
Alfa
AF:
0.574
Hom.:
3058
Bravo
AF:
0.599
Asia WGS
AF:
0.719
AC:
2501
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
6.3
DANN
Benign
0.53

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: rs9275535; hg19: chr6-32675789; API