chr11-86147496-G-A

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 0.728 in 152,132 control chromosomes in the GnomAD database, including 40,932 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 0.73 ( 40932 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0180
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.728
AC:
110645
AN:
152012
Hom.:
40890
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.869
Gnomad AMI
AF:
0.599
Gnomad AMR
AF:
0.669
Gnomad ASJ
AF:
0.692
Gnomad EAS
AF:
0.590
Gnomad SAS
AF:
0.653
Gnomad FIN
AF:
0.654
Gnomad MID
AF:
0.649
Gnomad NFE
AF:
0.686
Gnomad OTH
AF:
0.724
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.728
AC:
110744
AN:
152132
Hom.:
40932
Cov.:
32
AF XY:
0.724
AC XY:
53806
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.870
Gnomad4 AMR
AF:
0.668
Gnomad4 ASJ
AF:
0.692
Gnomad4 EAS
AF:
0.589
Gnomad4 SAS
AF:
0.654
Gnomad4 FIN
AF:
0.654
Gnomad4 NFE
AF:
0.686
Gnomad4 OTH
AF:
0.723
Alfa
AF:
0.693
Hom.:
55271
Bravo
AF:
0.734
Asia WGS
AF:
0.611
AC:
2124
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.3
DANN
Benign
0.40

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: rs7941541; hg19: chr11-85858538; API