chr9-84226487-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 0.72 in 151,876 control chromosomes in the GnomAD database, including 40,772 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 0.72 ( 40772 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.511
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 = 0.905 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:
0.719
AC:
109166
AN:
151758
Hom.:
40697
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.913
Gnomad AMI
AF:
0.523
Gnomad AMR
AF:
0.754
Gnomad ASJ
AF:
0.650
Gnomad EAS
AF:
0.892
Gnomad SAS
AF:
0.811
Gnomad FIN
AF:
0.633
Gnomad MID
AF:
0.582
Gnomad NFE
AF:
0.595
Gnomad OTH
AF:
0.696
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.720
AC:
109304
AN:
151876
Hom.:
40772
Cov.:
30
AF XY:
0.722
AC XY:
53600
AN XY:
74192
show subpopulations
Gnomad4 AFR
AF:
0.913
Gnomad4 AMR
AF:
0.755
Gnomad4 ASJ
AF:
0.650
Gnomad4 EAS
AF:
0.892
Gnomad4 SAS
AF:
0.811
Gnomad4 FIN
AF:
0.633
Gnomad4 NFE
AF:
0.595
Gnomad4 OTH
AF:
0.700
Alfa
AF:
0.623
Hom.:
40301
Bravo
AF:
0.736
Asia WGS
AF:
0.866
AC:
3008
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.74
DANN
Benign
0.38

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: rs10780656; hg19: chr9-86841402; API