rs11801558

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 0.17 in 152,136 control chromosomes in the GnomAD database, including 3,404 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 0.17 ( 3404 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.124
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 (AFR) allele frequency at 95% confidence interval = 0.364 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:
0.170
AC:
25802
AN:
152018
Hom.:
3390
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.369
Gnomad AMI
AF:
0.0724
Gnomad AMR
AF:
0.0818
Gnomad ASJ
AF:
0.110
Gnomad EAS
AF:
0.000384
Gnomad SAS
AF:
0.0981
Gnomad FIN
AF:
0.106
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.102
Gnomad OTH
AF:
0.150
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.170
AC:
25853
AN:
152136
Hom.:
3404
Cov.:
33
AF XY:
0.167
AC XY:
12389
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.369
Gnomad4 AMR
AF:
0.0816
Gnomad4 ASJ
AF:
0.110
Gnomad4 EAS
AF:
0.000385
Gnomad4 SAS
AF:
0.0976
Gnomad4 FIN
AF:
0.106
Gnomad4 NFE
AF:
0.102
Gnomad4 OTH
AF:
0.149
Alfa
AF:
0.107
Hom.:
1834
Bravo
AF:
0.174
Asia WGS
AF:
0.0620
AC:
219
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
1.6
DANN
Benign
0.38

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: rs11801558; hg19: chr1-158338906; API