rs11228551

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 0.24 in 152,100 control chromosomes in the GnomAD database, including 4,845 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 0.24 ( 4845 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.531
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 (NFE) allele frequency at 95% confidence interval = 0.297 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:
0.240
AC:
36499
AN:
151982
Hom.:
4846
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.187
Gnomad AMI
AF:
0.282
Gnomad AMR
AF:
0.196
Gnomad ASJ
AF:
0.263
Gnomad EAS
AF:
0.0173
Gnomad SAS
AF:
0.107
Gnomad FIN
AF:
0.280
Gnomad MID
AF:
0.256
Gnomad NFE
AF:
0.300
Gnomad OTH
AF:
0.269
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.240
AC:
36511
AN:
152100
Hom.:
4845
Cov.:
32
AF XY:
0.235
AC XY:
17466
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.187
Gnomad4 AMR
AF:
0.196
Gnomad4 ASJ
AF:
0.263
Gnomad4 EAS
AF:
0.0174
Gnomad4 SAS
AF:
0.107
Gnomad4 FIN
AF:
0.280
Gnomad4 NFE
AF:
0.300
Gnomad4 OTH
AF:
0.268
Alfa
AF:
0.271
Hom.:
758
Bravo
AF:
0.235
Asia WGS
AF:
0.119
AC:
413
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
0.15
DANN
Benign
0.58

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: rs11228551; hg19: chr11-68954994; API