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GeneBe

rs9308868

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 0.455 in 151,840 control chromosomes in the GnomAD database, including 16,685 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 0.45 ( 16685 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.78
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=-0.96).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.7 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:
0.455
AC:
69033
AN:
151722
Hom.:
16675
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.297
Gnomad AMI
AF:
0.387
Gnomad AMR
AF:
0.414
Gnomad ASJ
AF:
0.574
Gnomad EAS
AF:
0.651
Gnomad SAS
AF:
0.721
Gnomad FIN
AF:
0.496
Gnomad MID
AF:
0.478
Gnomad NFE
AF:
0.516
Gnomad OTH
AF:
0.434
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.455
AC:
69065
AN:
151840
Hom.:
16685
Cov.:
31
AF XY:
0.459
AC XY:
34031
AN XY:
74180
show subpopulations
Gnomad4 AFR
AF:
0.297
Gnomad4 AMR
AF:
0.414
Gnomad4 ASJ
AF:
0.574
Gnomad4 EAS
AF:
0.651
Gnomad4 SAS
AF:
0.720
Gnomad4 FIN
AF:
0.496
Gnomad4 NFE
AF:
0.516
Gnomad4 OTH
AF:
0.440
Alfa
AF:
0.509
Hom.:
33071
Bravo
AF:
0.435
Asia WGS
AF:
0.665
AC:
2312
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
Cadd
Benign
0.0090
Dann
Benign
0.63

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: rs9308868; hg19: chr2-104361420; API