rs11246226

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 0.48 in 152,170 control chromosomes in the GnomAD database, including 17,968 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 0.48 ( 17968 hom., cov: 35)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.864
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=-0.82).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 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:
0.480
AC:
73011
AN:
152052
Hom.:
17958
Cov.:
35
show subpopulations
Gnomad AFR
AF:
0.379
Gnomad AMI
AF:
0.566
Gnomad AMR
AF:
0.526
Gnomad ASJ
AF:
0.485
Gnomad EAS
AF:
0.729
Gnomad SAS
AF:
0.586
Gnomad FIN
AF:
0.474
Gnomad MID
AF:
0.459
Gnomad NFE
AF:
0.504
Gnomad OTH
AF:
0.478
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.480
AC:
73065
AN:
152170
Hom.:
17968
Cov.:
35
AF XY:
0.483
AC XY:
35956
AN XY:
74396
show subpopulations
Gnomad4 AFR
AF:
0.380
Gnomad4 AMR
AF:
0.526
Gnomad4 ASJ
AF:
0.485
Gnomad4 EAS
AF:
0.730
Gnomad4 SAS
AF:
0.585
Gnomad4 FIN
AF:
0.474
Gnomad4 NFE
AF:
0.505
Gnomad4 OTH
AF:
0.476
Alfa
AF:
0.502
Hom.:
21345
Bravo
AF:
0.479
Asia WGS
AF:
0.616
AC:
2142
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
1.0
DANN
Benign
0.87

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: rs11246226; hg19: chr11-641191; API