chr11-58345478-C-T

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 0.715 in 151,800 control chromosomes in the GnomAD database, including 39,464 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 0.72 ( 39464 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.190
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=-1.0).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.715
AC:
108465
AN:
151680
Hom.:
39411
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.844
Gnomad AMI
AF:
0.680
Gnomad AMR
AF:
0.752
Gnomad ASJ
AF:
0.653
Gnomad EAS
AF:
0.854
Gnomad SAS
AF:
0.696
Gnomad FIN
AF:
0.662
Gnomad MID
AF:
0.655
Gnomad NFE
AF:
0.631
Gnomad OTH
AF:
0.725
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.715
AC:
108579
AN:
151800
Hom.:
39464
Cov.:
31
AF XY:
0.718
AC XY:
53270
AN XY:
74194
show subpopulations
Gnomad4 AFR
AF:
0.844
Gnomad4 AMR
AF:
0.752
Gnomad4 ASJ
AF:
0.653
Gnomad4 EAS
AF:
0.854
Gnomad4 SAS
AF:
0.696
Gnomad4 FIN
AF:
0.662
Gnomad4 NFE
AF:
0.631
Gnomad4 OTH
AF:
0.726
Alfa
AF:
0.650
Hom.:
42402
Bravo
AF:
0.730
Asia WGS
AF:
0.743
AC:
2584
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
2.6
DANN
Benign
0.39

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: rs1938651; hg19: chr11-58112951; API