rs17410

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 0.478 in 111,420 control chromosomes in the GnomAD database, including 9,360 homozygotes. There are 15,732 hemizygotes in GnomAD. 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 0.48 ( 9360 hom., 15732 hem., cov: 24)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.306

Publications

2 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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 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:
0.478
AC:
53190
AN:
111367
Hom.:
9356
Cov.:
24
show subpopulations
Gnomad AFR
AF:
0.618
Gnomad AMI
AF:
0.187
Gnomad AMR
AF:
0.479
Gnomad ASJ
AF:
0.392
Gnomad EAS
AF:
0.338
Gnomad SAS
AF:
0.375
Gnomad FIN
AF:
0.444
Gnomad MID
AF:
0.287
Gnomad NFE
AF:
0.423
Gnomad OTH
AF:
0.491
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.478
AC:
53246
AN:
111420
Hom.:
9360
Cov.:
24
AF XY:
0.467
AC XY:
15732
AN XY:
33676
show subpopulations
African (AFR)
AF:
0.618
AC:
18973
AN:
30681
American (AMR)
AF:
0.479
AC:
5106
AN:
10657
Ashkenazi Jewish (ASJ)
AF:
0.392
AC:
1031
AN:
2631
East Asian (EAS)
AF:
0.338
AC:
1176
AN:
3480
South Asian (SAS)
AF:
0.373
AC:
995
AN:
2669
European-Finnish (FIN)
AF:
0.444
AC:
2691
AN:
6065
Middle Eastern (MID)
AF:
0.306
AC:
66
AN:
216
European-Non Finnish (NFE)
AF:
0.423
AC:
22329
AN:
52818
Other (OTH)
AF:
0.493
AC:
753
AN:
1528
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1002
2004
3006
4008
5010
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
502
1004
1506
2008
2510
<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:
0.464
Hom.:
3648
Bravo
AF:
0.493

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
5.6
DANN
Benign
0.49
PhyloP100
0.31

Splicing

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

Publications

Other links and lift over

dbSNP: rs17410; hg19: chrX-144021193; API