rs11734132

Positions:

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 0.173 in 152,220 control chromosomes in the GnomAD database, including 2,742 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 ( 2742 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.361
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=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 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:
0.173
AC:
26287
AN:
152104
Hom.:
2742
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.112
Gnomad AMI
AF:
0.124
Gnomad AMR
AF:
0.202
Gnomad ASJ
AF:
0.117
Gnomad EAS
AF:
0.557
Gnomad SAS
AF:
0.169
Gnomad FIN
AF:
0.193
Gnomad MID
AF:
0.150
Gnomad NFE
AF:
0.175
Gnomad OTH
AF:
0.178
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.173
AC:
26284
AN:
152220
Hom.:
2742
Cov.:
33
AF XY:
0.174
AC XY:
12960
AN XY:
74424
show subpopulations
Gnomad4 AFR
AF:
0.112
Gnomad4 AMR
AF:
0.202
Gnomad4 ASJ
AF:
0.117
Gnomad4 EAS
AF:
0.557
Gnomad4 SAS
AF:
0.169
Gnomad4 FIN
AF:
0.193
Gnomad4 NFE
AF:
0.175
Gnomad4 OTH
AF:
0.175
Alfa
AF:
0.185
Hom.:
1722
Bravo
AF:
0.175
Asia WGS
AF:
0.266
AC:
926
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
3.8
DANN
Benign
0.63

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: rs11734132; hg19: chr4-6891519; API