chr11-130477295-G-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 0.384 in 152,044 control chromosomes in the GnomAD database, including 11,807 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 0.38 ( 11807 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0970
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 (AFR) allele frequency at 95% confidence interval = 0.503 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:
0.384
AC:
58333
AN:
151926
Hom.:
11787
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.508
Gnomad AMI
AF:
0.360
Gnomad AMR
AF:
0.357
Gnomad ASJ
AF:
0.350
Gnomad EAS
AF:
0.482
Gnomad SAS
AF:
0.419
Gnomad FIN
AF:
0.361
Gnomad MID
AF:
0.399
Gnomad NFE
AF:
0.310
Gnomad OTH
AF:
0.384
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.384
AC:
58402
AN:
152044
Hom.:
11807
Cov.:
32
AF XY:
0.387
AC XY:
28749
AN XY:
74300
show subpopulations
Gnomad4 AFR
AF:
0.509
Gnomad4 AMR
AF:
0.357
Gnomad4 ASJ
AF:
0.350
Gnomad4 EAS
AF:
0.481
Gnomad4 SAS
AF:
0.418
Gnomad4 FIN
AF:
0.361
Gnomad4 NFE
AF:
0.310
Gnomad4 OTH
AF:
0.386
Alfa
AF:
0.328
Hom.:
17298
Bravo
AF:
0.389
Asia WGS
AF:
0.451
AC:
1563
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
1.8
DANN
Benign
0.55

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: rs4937523; hg19: chr11-130347190; API