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GeneBe

rs9879257

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 0.17 in 152,106 control chromosomes in the GnomAD database, including 5,675 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 0.17 ( 5675 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.80
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=-1.06).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.507 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:
0.170
AC:
25857
AN:
151988
Hom.:
5657
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.513
Gnomad AMI
AF:
0.0231
Gnomad AMR
AF:
0.0744
Gnomad ASJ
AF:
0.0228
Gnomad EAS
AF:
0.000577
Gnomad SAS
AF:
0.0104
Gnomad FIN
AF:
0.0441
Gnomad MID
AF:
0.0506
Gnomad NFE
AF:
0.0392
Gnomad OTH
AF:
0.122
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.170
AC:
25924
AN:
152106
Hom.:
5675
Cov.:
31
AF XY:
0.163
AC XY:
12124
AN XY:
74378
show subpopulations
Gnomad4 AFR
AF:
0.513
Gnomad4 AMR
AF:
0.0742
Gnomad4 ASJ
AF:
0.0228
Gnomad4 EAS
AF:
0.000578
Gnomad4 SAS
AF:
0.0102
Gnomad4 FIN
AF:
0.0441
Gnomad4 NFE
AF:
0.0392
Gnomad4 OTH
AF:
0.120
Alfa
AF:
0.0599
Hom.:
216
Bravo
AF:
0.192
Asia WGS
AF:
0.0420
AC:
148
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
Cadd
Benign
0.24
Dann
Benign
0.25

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: rs9879257; hg19: chr3-46158717; API