rs9810857

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 0.404 in 152,102 control chromosomes in the GnomAD database, including 14,407 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 0.40 ( 14407 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.233

Publications

20 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=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 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:
0.404
AC:
61451
AN:
151984
Hom.:
14403
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.189
Gnomad AMI
AF:
0.413
Gnomad AMR
AF:
0.377
Gnomad ASJ
AF:
0.440
Gnomad EAS
AF:
0.112
Gnomad SAS
AF:
0.398
Gnomad FIN
AF:
0.566
Gnomad MID
AF:
0.405
Gnomad NFE
AF:
0.537
Gnomad OTH
AF:
0.427
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.404
AC:
61455
AN:
152102
Hom.:
14407
Cov.:
32
AF XY:
0.400
AC XY:
29735
AN XY:
74370
show subpopulations
African (AFR)
AF:
0.189
AC:
7828
AN:
41504
American (AMR)
AF:
0.376
AC:
5746
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.440
AC:
1528
AN:
3472
East Asian (EAS)
AF:
0.112
AC:
578
AN:
5178
South Asian (SAS)
AF:
0.399
AC:
1921
AN:
4814
European-Finnish (FIN)
AF:
0.566
AC:
5979
AN:
10570
Middle Eastern (MID)
AF:
0.408
AC:
120
AN:
294
European-Non Finnish (NFE)
AF:
0.537
AC:
36483
AN:
67968
Other (OTH)
AF:
0.424
AC:
895
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1698
3396
5094
6792
8490
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
570
1140
1710
2280
2850
<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:
0.482
Hom.:
65519
Bravo
AF:
0.375
Asia WGS
AF:
0.234
AC:
815
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
2.0
DANN
Benign
0.38
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: rs9810857; hg19: chr3-142982899; API