rs11231017

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 0.298 in 152,074 control chromosomes in the GnomAD database, including 7,903 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 ( 7903 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.793
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=-0.97).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.38 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:
0.299
AC:
45397
AN:
151956
Hom.:
7909
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.112
Gnomad AMI
AF:
0.325
Gnomad AMR
AF:
0.295
Gnomad ASJ
AF:
0.467
Gnomad EAS
AF:
0.298
Gnomad SAS
AF:
0.387
Gnomad FIN
AF:
0.385
Gnomad MID
AF:
0.408
Gnomad NFE
AF:
0.384
Gnomad OTH
AF:
0.320
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.298
AC:
45394
AN:
152074
Hom.:
7903
Cov.:
32
AF XY:
0.300
AC XY:
22272
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.112
Gnomad4 AMR
AF:
0.295
Gnomad4 ASJ
AF:
0.467
Gnomad4 EAS
AF:
0.298
Gnomad4 SAS
AF:
0.387
Gnomad4 FIN
AF:
0.385
Gnomad4 NFE
AF:
0.384
Gnomad4 OTH
AF:
0.319
Alfa
AF:
0.374
Hom.:
17216
Bravo
AF:
0.284
Asia WGS
AF:
0.352
AC:
1221
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.086
DANN
Benign
0.27

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: rs11231017; hg19: chr11-62061349; API