11-123886178-C-G

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 0.626 in 151,426 control chromosomes in the GnomAD database, including 30,372 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 0.63 ( 30372 hom., cov: 28)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.22
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=-1.05).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 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:
0.626
AC:
94747
AN:
151314
Hom.:
30318
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.765
Gnomad AMI
AF:
0.611
Gnomad AMR
AF:
0.648
Gnomad ASJ
AF:
0.640
Gnomad EAS
AF:
0.572
Gnomad SAS
AF:
0.540
Gnomad FIN
AF:
0.572
Gnomad MID
AF:
0.563
Gnomad NFE
AF:
0.556
Gnomad OTH
AF:
0.606
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.626
AC:
94856
AN:
151426
Hom.:
30372
Cov.:
28
AF XY:
0.626
AC XY:
46312
AN XY:
73960
show subpopulations
Gnomad4 AFR
AF:
0.765
Gnomad4 AMR
AF:
0.648
Gnomad4 ASJ
AF:
0.640
Gnomad4 EAS
AF:
0.572
Gnomad4 SAS
AF:
0.542
Gnomad4 FIN
AF:
0.572
Gnomad4 NFE
AF:
0.556
Gnomad4 OTH
AF:
0.601
Alfa
AF:
0.583
Hom.:
3160
Bravo
AF:
0.640
Asia WGS
AF:
0.554
AC:
1926
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
CADD
Benign
0.020
DANN
Benign
0.59

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: rs7941883; hg19: chr11-123756885; API