rs2417531

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 0.185 in 151,994 control chromosomes in the GnomAD database, including 3,356 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 0.19 ( 3356 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.567
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=-1.01).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 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:
0.185
AC:
28135
AN:
151876
Hom.:
3353
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.322
Gnomad AMI
AF:
0.142
Gnomad AMR
AF:
0.157
Gnomad ASJ
AF:
0.181
Gnomad EAS
AF:
0.345
Gnomad SAS
AF:
0.173
Gnomad FIN
AF:
0.102
Gnomad MID
AF:
0.259
Gnomad NFE
AF:
0.110
Gnomad OTH
AF:
0.189
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.185
AC:
28175
AN:
151994
Hom.:
3356
Cov.:
30
AF XY:
0.185
AC XY:
13738
AN XY:
74284
show subpopulations
Gnomad4 AFR
AF:
0.322
Gnomad4 AMR
AF:
0.157
Gnomad4 ASJ
AF:
0.181
Gnomad4 EAS
AF:
0.345
Gnomad4 SAS
AF:
0.174
Gnomad4 FIN
AF:
0.102
Gnomad4 NFE
AF:
0.110
Gnomad4 OTH
AF:
0.190
Alfa
AF:
0.135
Hom.:
2566
Bravo
AF:
0.198
Asia WGS
AF:
0.282
AC:
978
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.35
DANN
Benign
0.24

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: rs2417531; hg19: chr9-107263182; API