rs11853883

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 0.296 in 152,002 control chromosomes in the GnomAD database, including 6,943 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 0.30 ( 6943 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0690
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=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.569 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:
0.296
AC:
44913
AN:
151884
Hom.:
6937
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.288
Gnomad AMI
AF:
0.507
Gnomad AMR
AF:
0.337
Gnomad ASJ
AF:
0.364
Gnomad EAS
AF:
0.587
Gnomad SAS
AF:
0.235
Gnomad FIN
AF:
0.217
Gnomad MID
AF:
0.310
Gnomad NFE
AF:
0.279
Gnomad OTH
AF:
0.323
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.296
AC:
44938
AN:
152002
Hom.:
6943
Cov.:
31
AF XY:
0.294
AC XY:
21828
AN XY:
74312
show subpopulations
Gnomad4 AFR
AF:
0.288
Gnomad4 AMR
AF:
0.336
Gnomad4 ASJ
AF:
0.364
Gnomad4 EAS
AF:
0.587
Gnomad4 SAS
AF:
0.235
Gnomad4 FIN
AF:
0.217
Gnomad4 NFE
AF:
0.279
Gnomad4 OTH
AF:
0.320
Alfa
AF:
0.274
Hom.:
4666
Bravo
AF:
0.310
Asia WGS
AF:
0.369
AC:
1283
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
4.2
DANN
Benign
0.43

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: rs11853883; hg19: chr15-94719916; API