rs2282079

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 0.0547 in 152,134 control chromosomes in the GnomAD database, including 277 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 0.055 ( 277 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.40
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=-0.76).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.106 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:
0.0547
AC:
8320
AN:
152016
Hom.:
276
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0813
Gnomad AMI
AF:
0.0132
Gnomad AMR
AF:
0.0620
Gnomad ASJ
AF:
0.0594
Gnomad EAS
AF:
0.114
Gnomad SAS
AF:
0.0197
Gnomad FIN
AF:
0.0233
Gnomad MID
AF:
0.114
Gnomad NFE
AF:
0.0395
Gnomad OTH
AF:
0.0630
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0547
AC:
8327
AN:
152134
Hom.:
277
Cov.:
32
AF XY:
0.0539
AC XY:
4012
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.0813
Gnomad4 AMR
AF:
0.0620
Gnomad4 ASJ
AF:
0.0594
Gnomad4 EAS
AF:
0.114
Gnomad4 SAS
AF:
0.0201
Gnomad4 FIN
AF:
0.0233
Gnomad4 NFE
AF:
0.0395
Gnomad4 OTH
AF:
0.0629
Alfa
AF:
0.0443
Hom.:
163
Bravo
AF:
0.0609
Asia WGS
AF:
0.0590
AC:
207
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
CADD
Benign
16
DANN
Benign
0.78

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: rs2282079; hg19: chr9-37036247; API