9-25667521-G-C

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 0.136 in 151,948 control chromosomes in the GnomAD database, including 1,436 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 0.14 ( 1436 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.54
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=-0.99).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.15 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:
0.136
AC:
20629
AN:
151830
Hom.:
1435
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.120
Gnomad AMI
AF:
0.105
Gnomad AMR
AF:
0.122
Gnomad ASJ
AF:
0.0953
Gnomad EAS
AF:
0.0511
Gnomad SAS
AF:
0.0734
Gnomad FIN
AF:
0.203
Gnomad MID
AF:
0.114
Gnomad NFE
AF:
0.152
Gnomad OTH
AF:
0.132
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.136
AC:
20643
AN:
151948
Hom.:
1436
Cov.:
33
AF XY:
0.136
AC XY:
10083
AN XY:
74250
show subpopulations
Gnomad4 AFR
AF:
0.120
Gnomad4 AMR
AF:
0.121
Gnomad4 ASJ
AF:
0.0953
Gnomad4 EAS
AF:
0.0512
Gnomad4 SAS
AF:
0.0730
Gnomad4 FIN
AF:
0.203
Gnomad4 NFE
AF:
0.152
Gnomad4 OTH
AF:
0.132
Alfa
AF:
0.0651
Hom.:
87
Bravo
AF:
0.130
Asia WGS
AF:
0.0610
AC:
212
AN:
3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.57
DANN
Benign
0.70

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: rs13290968; hg19: chr9-25667519; API