rs17309585

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.266 in 151,958 control chromosomes in the GnomAD database, including 6,671 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 0.27 ( 6671 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.400
Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.3).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 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:
0.266
AC:
40378
AN:
151840
Hom.:
6671
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0982
Gnomad AMI
AF:
0.391
Gnomad AMR
AF:
0.237
Gnomad ASJ
AF:
0.352
Gnomad EAS
AF:
0.0253
Gnomad SAS
AF:
0.267
Gnomad FIN
AF:
0.375
Gnomad MID
AF:
0.429
Gnomad NFE
AF:
0.368
Gnomad OTH
AF:
0.290
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.266
AC:
40388
AN:
151958
Hom.:
6671
Cov.:
31
AF XY:
0.264
AC XY:
19573
AN XY:
74244
show subpopulations
Gnomad4 AFR
AF:
0.0981
Gnomad4 AMR
AF:
0.237
Gnomad4 ASJ
AF:
0.352
Gnomad4 EAS
AF:
0.0256
Gnomad4 SAS
AF:
0.268
Gnomad4 FIN
AF:
0.375
Gnomad4 NFE
AF:
0.368
Gnomad4 OTH
AF:
0.290
Alfa
AF:
0.350
Hom.:
20275
Bravo
AF:
0.250
Asia WGS
AF:
0.166
AC:
577
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.30
CADD
Benign
15
DANN
Benign
0.60

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: rs17309585; hg19: chr8-108866822; API