rs17117533

Variant summary

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

The ENST00000658937.2(ENSG00000286973):​n.509+23889G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,112 control chromosomes in the GnomAD database, including 3,894 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 0.22 ( 3894 hom., cov: 32)

Consequence

ENSG00000286973
ENST00000658937.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.245

Publications

2 publications found
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 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
ENSG00000286973ENST00000658937.2 linkn.509+23889G>C intron_variant Intron 1 of 2
ENSG00000286973ENST00000844005.1 linkn.600+9682G>C intron_variant Intron 2 of 3
ENSG00000286973ENST00000844006.1 linkn.471+23889G>C intron_variant Intron 1 of 3

Frequencies

GnomAD3 genomes
AF:
0.219
AC:
33266
AN:
151994
Hom.:
3894
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.287
Gnomad AMI
AF:
0.0954
Gnomad AMR
AF:
0.159
Gnomad ASJ
AF:
0.233
Gnomad EAS
AF:
0.0252
Gnomad SAS
AF:
0.205
Gnomad FIN
AF:
0.239
Gnomad MID
AF:
0.259
Gnomad NFE
AF:
0.205
Gnomad OTH
AF:
0.191
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.219
AC:
33265
AN:
152112
Hom.:
3894
Cov.:
32
AF XY:
0.219
AC XY:
16292
AN XY:
74354
show subpopulations
African (AFR)
AF:
0.287
AC:
11884
AN:
41470
American (AMR)
AF:
0.158
AC:
2419
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.233
AC:
810
AN:
3472
East Asian (EAS)
AF:
0.0251
AC:
130
AN:
5178
South Asian (SAS)
AF:
0.205
AC:
989
AN:
4824
European-Finnish (FIN)
AF:
0.239
AC:
2529
AN:
10570
Middle Eastern (MID)
AF:
0.255
AC:
75
AN:
294
European-Non Finnish (NFE)
AF:
0.205
AC:
13944
AN:
67994
Other (OTH)
AF:
0.188
AC:
398
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1314
2629
3943
5258
6572
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
346
692
1038
1384
1730
<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:
0.0747
Hom.:
99
Bravo
AF:
0.212
Asia WGS
AF:
0.141
AC:
492
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
3.0
DANN
Benign
0.77
PhyloP100
-0.24

Splicing

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

Publications

Other links and lift over

dbSNP: rs17117533; hg19: chr15-24026609; API