rs9276298

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 0.8 in 152,130 control chromosomes in the GnomAD database, including 48,951 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 0.80 ( 48951 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0170
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 (SAS) allele frequency at 95% confidence interval = 0.894 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:
0.800
AC:
121682
AN:
152012
Hom.:
48914
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.822
Gnomad AMI
AF:
0.816
Gnomad AMR
AF:
0.825
Gnomad ASJ
AF:
0.842
Gnomad EAS
AF:
0.915
Gnomad SAS
AF:
0.917
Gnomad FIN
AF:
0.770
Gnomad MID
AF:
0.851
Gnomad NFE
AF:
0.766
Gnomad OTH
AF:
0.844
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.800
AC:
121773
AN:
152130
Hom.:
48951
Cov.:
32
AF XY:
0.803
AC XY:
59705
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.822
Gnomad4 AMR
AF:
0.825
Gnomad4 ASJ
AF:
0.842
Gnomad4 EAS
AF:
0.915
Gnomad4 SAS
AF:
0.917
Gnomad4 FIN
AF:
0.770
Gnomad4 NFE
AF:
0.766
Gnomad4 OTH
AF:
0.847
Alfa
AF:
0.776
Hom.:
13425
Bravo
AF:
0.803
Asia WGS
AF:
0.907
AC:
3152
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
2.8
DANN
Benign
0.62

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: rs9276298; hg19: chr6-32703021; API