rs17534202

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 0.401 in 152,078 control chromosomes in the GnomAD database, including 14,490 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 0.40 ( 14490 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.47
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.402
AC:
61030
AN:
151960
Hom.:
14486
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.155
Gnomad AMI
AF:
0.520
Gnomad AMR
AF:
0.385
Gnomad ASJ
AF:
0.542
Gnomad EAS
AF:
0.216
Gnomad SAS
AF:
0.409
Gnomad FIN
AF:
0.525
Gnomad MID
AF:
0.497
Gnomad NFE
AF:
0.540
Gnomad OTH
AF:
0.420
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.401
AC:
61035
AN:
152078
Hom.:
14490
Cov.:
32
AF XY:
0.400
AC XY:
29767
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.155
Gnomad4 AMR
AF:
0.384
Gnomad4 ASJ
AF:
0.542
Gnomad4 EAS
AF:
0.216
Gnomad4 SAS
AF:
0.408
Gnomad4 FIN
AF:
0.525
Gnomad4 NFE
AF:
0.540
Gnomad4 OTH
AF:
0.424
Alfa
AF:
0.463
Hom.:
2197
Bravo
AF:
0.379
Asia WGS
AF:
0.310
AC:
1079
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.40
CADD
Benign
19
DANN
Benign
0.82

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: rs17534202; hg19: chr1-203281175; API