9-136932121-T-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 0.78 in 152,034 control chromosomes in the GnomAD database, including 46,727 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 0.78 ( 46727 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.40
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=-1.02).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.875 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:
0.780
AC:
118547
AN:
151916
Hom.:
46688
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.883
Gnomad AMI
AF:
0.801
Gnomad AMR
AF:
0.651
Gnomad ASJ
AF:
0.752
Gnomad EAS
AF:
0.869
Gnomad SAS
AF:
0.798
Gnomad FIN
AF:
0.755
Gnomad MID
AF:
0.712
Gnomad NFE
AF:
0.745
Gnomad OTH
AF:
0.754
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.780
AC:
118645
AN:
152034
Hom.:
46727
Cov.:
32
AF XY:
0.780
AC XY:
57980
AN XY:
74318
show subpopulations
Gnomad4 AFR
AF:
0.883
Gnomad4 AMR
AF:
0.651
Gnomad4 ASJ
AF:
0.752
Gnomad4 EAS
AF:
0.869
Gnomad4 SAS
AF:
0.797
Gnomad4 FIN
AF:
0.755
Gnomad4 NFE
AF:
0.745
Gnomad4 OTH
AF:
0.758
Alfa
AF:
0.785
Hom.:
6730
Bravo
AF:
0.775
Asia WGS
AF:
0.809
AC:
2811
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.87
DANN
Benign
0.30

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: rs4880166; hg19: chr9-139826573; API