GeneBe

ENST00000556865.1:n.760+572G>A

Variant names:

Variant summary

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

The ENST00000556865.1(C15orf32):​n.760+572G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,064 control chromosomes in the GnomAD database, including 10,777 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 0.37 ( 10777 hom., cov: 33)

Consequence

C15orf32
ENST00000556865.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.178

Publications

2 publications found
Variant links:
Genes affected
C15orf32 (HGNC:26549): (chromosome 15 putative open reading frame 32)

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=-1.03).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
C15orf32NR_161370.1 linkn.966+610G>A intron_variant Intron 2 of 2
C15orf32NR_161371.1 linkn.1004+572G>A intron_variant Intron 2 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
C15orf32ENST00000556865.1 linkn.760+572G>A intron_variant Intron 2 of 2 1
C15orf32ENST00000624458.1 linkn.989+610G>A intron_variant Intron 2 of 2 1

Frequencies

GnomAD3 genomes
AF:
0.370
AC:
56173
AN:
151946
Hom.:
10771
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.450
Gnomad AMI
AF:
0.273
Gnomad AMR
AF:
0.426
Gnomad ASJ
AF:
0.309
Gnomad EAS
AF:
0.470
Gnomad SAS
AF:
0.398
Gnomad FIN
AF:
0.378
Gnomad MID
AF:
0.415
Gnomad NFE
AF:
0.301
Gnomad OTH
AF:
0.369
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.370
AC:
56199
AN:
152064
Hom.:
10777
Cov.:
33
AF XY:
0.377
AC XY:
28045
AN XY:
74330
show subpopulations
African (AFR)
AF:
0.450
AC:
18646
AN:
41464
American (AMR)
AF:
0.426
AC:
6518
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
0.309
AC:
1074
AN:
3472
East Asian (EAS)
AF:
0.470
AC:
2431
AN:
5174
South Asian (SAS)
AF:
0.396
AC:
1907
AN:
4816
European-Finnish (FIN)
AF:
0.378
AC:
3994
AN:
10576
Middle Eastern (MID)
AF:
0.415
AC:
122
AN:
294
European-Non Finnish (NFE)
AF:
0.301
AC:
20484
AN:
67964
Other (OTH)
AF:
0.368
AC:
775
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1820
3640
5459
7279
9099
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
544
1088
1632
2176
2720
<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:
0.352
Hom.:
1618
Bravo
AF:
0.374
Asia WGS
AF:
0.455
AC:
1583
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
4.0
DANN
Benign
0.28
PhyloP100
-0.18
Mutation Taster
=100/0
polymorphism (auto)

Splicing

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

Publications

Other links and lift over

dbSNP: rs12441404; hg19: chr15-93016912; API