rs11128275

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 0.456 in 152,006 control chromosomes in the GnomAD database, including 17,548 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 0.46 ( 17548 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.11
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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 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:
0.456
AC:
69225
AN:
151888
Hom.:
17534
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.225
Gnomad AMI
AF:
0.513
Gnomad AMR
AF:
0.568
Gnomad ASJ
AF:
0.452
Gnomad EAS
AF:
0.705
Gnomad SAS
AF:
0.602
Gnomad FIN
AF:
0.565
Gnomad MID
AF:
0.456
Gnomad NFE
AF:
0.524
Gnomad OTH
AF:
0.460
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.456
AC:
69253
AN:
152006
Hom.:
17548
Cov.:
32
AF XY:
0.465
AC XY:
34554
AN XY:
74280
show subpopulations
Gnomad4 AFR
AF:
0.224
Gnomad4 AMR
AF:
0.569
Gnomad4 ASJ
AF:
0.452
Gnomad4 EAS
AF:
0.705
Gnomad4 SAS
AF:
0.602
Gnomad4 FIN
AF:
0.565
Gnomad4 NFE
AF:
0.524
Gnomad4 OTH
AF:
0.461
Alfa
AF:
0.508
Hom.:
16197
Bravo
AF:
0.447
Asia WGS
AF:
0.591
AC:
2054
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.24
DANN
Benign
0.64

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: rs11128275; hg19: chr3-72515960; API