rs13109457

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 0.257 in 151,830 control chromosomes in the GnomAD database, including 5,168 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 0.26 ( 5168 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.421
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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 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:
0.257
AC:
38991
AN:
151712
Hom.:
5166
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.236
Gnomad AMI
AF:
0.254
Gnomad AMR
AF:
0.233
Gnomad ASJ
AF:
0.187
Gnomad EAS
AF:
0.441
Gnomad SAS
AF:
0.302
Gnomad FIN
AF:
0.311
Gnomad MID
AF:
0.199
Gnomad NFE
AF:
0.254
Gnomad OTH
AF:
0.230
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.257
AC:
39004
AN:
151830
Hom.:
5168
Cov.:
31
AF XY:
0.259
AC XY:
19217
AN XY:
74188
show subpopulations
Gnomad4 AFR
AF:
0.236
Gnomad4 AMR
AF:
0.233
Gnomad4 ASJ
AF:
0.187
Gnomad4 EAS
AF:
0.441
Gnomad4 SAS
AF:
0.303
Gnomad4 FIN
AF:
0.311
Gnomad4 NFE
AF:
0.254
Gnomad4 OTH
AF:
0.228
Alfa
AF:
0.244
Hom.:
5724
Bravo
AF:
0.252
Asia WGS
AF:
0.315
AC:
1093
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
2.7
DANN
Benign
0.56

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: rs13109457; hg19: chr4-155514879; API