rs9275495

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 0.0908 in 151,872 control chromosomes in the GnomAD database, including 810 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 0.091 ( 810 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.147
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=-0.92).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0907
AC:
13768
AN:
151756
Hom.:
809
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0368
Gnomad AMI
AF:
0.142
Gnomad AMR
AF:
0.179
Gnomad ASJ
AF:
0.166
Gnomad EAS
AF:
0.0751
Gnomad SAS
AF:
0.0677
Gnomad FIN
AF:
0.109
Gnomad MID
AF:
0.0955
Gnomad NFE
AF:
0.0993
Gnomad OTH
AF:
0.0913
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0908
AC:
13787
AN:
151872
Hom.:
810
Cov.:
32
AF XY:
0.0926
AC XY:
6876
AN XY:
74270
show subpopulations
Gnomad4 AFR
AF:
0.0369
Gnomad4 AMR
AF:
0.179
Gnomad4 ASJ
AF:
0.166
Gnomad4 EAS
AF:
0.0753
Gnomad4 SAS
AF:
0.0676
Gnomad4 FIN
AF:
0.109
Gnomad4 NFE
AF:
0.0993
Gnomad4 OTH
AF:
0.0903
Alfa
AF:
0.0929
Hom.:
78
Bravo
AF:
0.0988
Asia WGS
AF:
0.0600
AC:
210
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
8.9
DANN
Benign
0.18

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: rs9275495; hg19: chr6-32673574; API