11-106286677-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 0.153 in 152,064 control chromosomes in the GnomAD database, including 1,990 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 0.15 ( 1990 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.545
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=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 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:
0.153
AC:
23293
AN:
151946
Hom.:
1986
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.200
Gnomad AMI
AF:
0.181
Gnomad AMR
AF:
0.165
Gnomad ASJ
AF:
0.205
Gnomad EAS
AF:
0.324
Gnomad SAS
AF:
0.160
Gnomad FIN
AF:
0.0709
Gnomad MID
AF:
0.209
Gnomad NFE
AF:
0.118
Gnomad OTH
AF:
0.173
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.153
AC:
23318
AN:
152064
Hom.:
1990
Cov.:
32
AF XY:
0.152
AC XY:
11286
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.200
Gnomad4 AMR
AF:
0.165
Gnomad4 ASJ
AF:
0.205
Gnomad4 EAS
AF:
0.324
Gnomad4 SAS
AF:
0.160
Gnomad4 FIN
AF:
0.0709
Gnomad4 NFE
AF:
0.118
Gnomad4 OTH
AF:
0.179
Alfa
AF:
0.135
Hom.:
2446
Bravo
AF:
0.164
Asia WGS
AF:
0.249
AC:
868
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.40
DANN
Benign
0.43

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: rs488212; hg19: chr11-106157404; API