rs9495441

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.0994 in 151,992 control chromosomes in the GnomAD database, including 1,306 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 0.099 ( 1306 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.232

Publications

0 publications found
Variant links:

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ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 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:
0.0994
AC:
15091
AN:
151874
Hom.:
1304
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.233
Gnomad AMI
AF:
0.110
Gnomad AMR
AF:
0.0582
Gnomad ASJ
AF:
0.0615
Gnomad EAS
AF:
0.00673
Gnomad SAS
AF:
0.0654
Gnomad FIN
AF:
0.0548
Gnomad MID
AF:
0.0443
Gnomad NFE
AF:
0.0464
Gnomad OTH
AF:
0.0842
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0994
AC:
15113
AN:
151992
Hom.:
1306
Cov.:
32
AF XY:
0.0980
AC XY:
7279
AN XY:
74308
show subpopulations
African (AFR)
AF:
0.232
AC:
9642
AN:
41486
American (AMR)
AF:
0.0581
AC:
886
AN:
15254
Ashkenazi Jewish (ASJ)
AF:
0.0615
AC:
213
AN:
3466
East Asian (EAS)
AF:
0.00675
AC:
35
AN:
5188
South Asian (SAS)
AF:
0.0663
AC:
320
AN:
4826
European-Finnish (FIN)
AF:
0.0548
AC:
580
AN:
10592
Middle Eastern (MID)
AF:
0.0408
AC:
12
AN:
294
European-Non Finnish (NFE)
AF:
0.0464
AC:
3149
AN:
67862
Other (OTH)
AF:
0.0833
AC:
176
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
665
1330
1996
2661
3326
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
156
312
468
624
780
<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:
0.0844
Hom.:
128
Bravo
AF:
0.105
Asia WGS
AF:
0.0540
AC:
186
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.9
DANN
Benign
0.53
PhyloP100
-0.23

Splicing

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

Publications

Other links and lift over

dbSNP: rs9495441; hg19: chr6-100207166; API