9-133278037-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 0.256 in 152,006 control chromosomes in the GnomAD database, including 5,226 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 0.26 ( 5226 hom., cov: 32)

Consequence

Unknown

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.212
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (Cadd=7.344).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.37 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:
0.256
AC:
38833
AN:
151888
Hom.:
5222
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.248
Gnomad AMI
AF:
0.0965
Gnomad AMR
AF:
0.378
Gnomad ASJ
AF:
0.276
Gnomad EAS
AF:
0.286
Gnomad SAS
AF:
0.216
Gnomad FIN
AF:
0.195
Gnomad MID
AF:
0.241
Gnomad NFE
AF:
0.244
Gnomad OTH
AF:
0.251
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.256
AC:
38852
AN:
152006
Hom.:
5226
Cov.:
32
AF XY:
0.256
AC XY:
19014
AN XY:
74288
show subpopulations
Gnomad4 AFR
AF:
0.247
Gnomad4 AMR
AF:
0.378
Gnomad4 ASJ
AF:
0.276
Gnomad4 EAS
AF:
0.285
Gnomad4 SAS
AF:
0.216
Gnomad4 FIN
AF:
0.195
Gnomad4 NFE
AF:
0.244
Gnomad4 OTH
AF:
0.250
Alfa
AF:
0.251
Hom.:
6896
Bravo
AF:
0.274

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
CADD
Benign
7.3

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: rs552148; hg19: -; API