rs1359536

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 0.0859 in 152,268 control chromosomes in the GnomAD database, including 576 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 0.086 ( 576 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.263
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=-0.86).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.111 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:
0.0860
AC:
13083
AN:
152150
Hom.:
577
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0761
Gnomad AMI
AF:
0.211
Gnomad AMR
AF:
0.115
Gnomad ASJ
AF:
0.101
Gnomad EAS
AF:
0.0901
Gnomad SAS
AF:
0.0608
Gnomad FIN
AF:
0.0493
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.0898
Gnomad OTH
AF:
0.0950
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0859
AC:
13081
AN:
152268
Hom.:
576
Cov.:
32
AF XY:
0.0837
AC XY:
6231
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.0759
Gnomad4 AMR
AF:
0.116
Gnomad4 ASJ
AF:
0.101
Gnomad4 EAS
AF:
0.0901
Gnomad4 SAS
AF:
0.0608
Gnomad4 FIN
AF:
0.0493
Gnomad4 NFE
AF:
0.0898
Gnomad4 OTH
AF:
0.0931
Alfa
AF:
0.0946
Hom.:
691
Bravo
AF:
0.0927
Asia WGS
AF:
0.0690
AC:
238
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
2.5
DANN
Benign
0.61

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: rs1359536; hg19: chr13-79275793; API