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GeneBe

rs17526278

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 0.142 in 151,920 control chromosomes in the GnomAD database, including 2,085 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 0.14 ( 2085 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.42
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=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 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:
0.142
AC:
21489
AN:
151802
Hom.:
2079
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.272
Gnomad AMI
AF:
0.178
Gnomad AMR
AF:
0.110
Gnomad ASJ
AF:
0.101
Gnomad EAS
AF:
0.0741
Gnomad SAS
AF:
0.0482
Gnomad FIN
AF:
0.0484
Gnomad MID
AF:
0.117
Gnomad NFE
AF:
0.0971
Gnomad OTH
AF:
0.145
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.142
AC:
21517
AN:
151920
Hom.:
2085
Cov.:
30
AF XY:
0.138
AC XY:
10245
AN XY:
74284
show subpopulations
Gnomad4 AFR
AF:
0.272
Gnomad4 AMR
AF:
0.110
Gnomad4 ASJ
AF:
0.101
Gnomad4 EAS
AF:
0.0743
Gnomad4 SAS
AF:
0.0478
Gnomad4 FIN
AF:
0.0484
Gnomad4 NFE
AF:
0.0971
Gnomad4 OTH
AF:
0.144
Alfa
AF:
0.0779
Hom.:
133
Bravo
AF:
0.155
Asia WGS
AF:
0.0730
AC:
255
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
Cadd
Benign
0.10
Dann
Benign
0.51

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: rs17526278; hg19: chr19-51357887; API