chr9-7540496-G-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.113 in 152,204 control chromosomes in the GnomAD database, including 1,338 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 0.11 ( 1338 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.140

Publications

3 publications found
Variant links:

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ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 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:
0.113
AC:
17162
AN:
152086
Hom.:
1333
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.213
Gnomad AMI
AF:
0.109
Gnomad AMR
AF:
0.0692
Gnomad ASJ
AF:
0.0536
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.0267
Gnomad FIN
AF:
0.0877
Gnomad MID
AF:
0.0828
Gnomad NFE
AF:
0.0845
Gnomad OTH
AF:
0.0856
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.113
AC:
17195
AN:
152204
Hom.:
1338
Cov.:
33
AF XY:
0.109
AC XY:
8112
AN XY:
74416
show subpopulations
African (AFR)
AF:
0.213
AC:
8846
AN:
41510
American (AMR)
AF:
0.0692
AC:
1058
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
0.0536
AC:
186
AN:
3470
East Asian (EAS)
AF:
0.000193
AC:
1
AN:
5184
South Asian (SAS)
AF:
0.0267
AC:
129
AN:
4830
European-Finnish (FIN)
AF:
0.0877
AC:
930
AN:
10600
Middle Eastern (MID)
AF:
0.0822
AC:
24
AN:
292
European-Non Finnish (NFE)
AF:
0.0845
AC:
5743
AN:
68000
Other (OTH)
AF:
0.0848
AC:
179
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
767
1534
2301
3068
3835
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
182
364
546
728
910
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.0897
Hom.:
889
Bravo
AF:
0.117
Asia WGS
AF:
0.0330
AC:
116
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.42
CADD
Benign
13
DANN
Benign
0.46
PhyloP100
-0.14

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs12349302; hg19: chr9-7540496; API