chr15-76572112-C-T

Variant summary

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

The NM_020843.4(SCAPER):​c.2838+2046G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.067 in 152,108 control chromosomes in the GnomAD database, including 381 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 0.067 ( 381 hom., cov: 32)

Consequence

SCAPER
NM_020843.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.994

Publications

4 publications found
Variant links:
Genes affected
SCAPER (HGNC:13081): (S-phase cyclin A associated protein in the ER) Predicted to enable nucleic acid binding activity and zinc ion binding activity. Located in cytosol and nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]
SCAPER Gene-Disease associations (from GenCC):
  • intellectual developmental disorder and retinitis pigmentosa; IDDRP
    Inheritance: AR Classification: STRONG, MODERATE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
  • retinitis pigmentosa
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • Bardet-Biedl syndrome
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

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=-0.8).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0665 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SCAPERNM_020843.4 linkc.2838+2046G>A intron_variant Intron 23 of 31 ENST00000563290.6 NP_065894.2 Q9BY12-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SCAPERENST00000563290.6 linkc.2838+2046G>A intron_variant Intron 23 of 31 5 NM_020843.4 ENSP00000454973.1 Q9BY12-1

Frequencies

GnomAD3 genomes
AF:
0.0670
AC:
10182
AN:
151990
Hom.:
381
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0681
Gnomad AMI
AF:
0.0385
Gnomad AMR
AF:
0.0700
Gnomad ASJ
AF:
0.116
Gnomad EAS
AF:
0.0350
Gnomad SAS
AF:
0.0576
Gnomad FIN
AF:
0.0614
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.0671
Gnomad OTH
AF:
0.0742
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0670
AC:
10186
AN:
152108
Hom.:
381
Cov.:
32
AF XY:
0.0674
AC XY:
5010
AN XY:
74342
show subpopulations
African (AFR)
AF:
0.0679
AC:
2820
AN:
41508
American (AMR)
AF:
0.0700
AC:
1068
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
0.116
AC:
403
AN:
3468
East Asian (EAS)
AF:
0.0351
AC:
182
AN:
5182
South Asian (SAS)
AF:
0.0577
AC:
278
AN:
4822
European-Finnish (FIN)
AF:
0.0614
AC:
649
AN:
10578
Middle Eastern (MID)
AF:
0.109
AC:
32
AN:
294
European-Non Finnish (NFE)
AF:
0.0671
AC:
4563
AN:
67972
Other (OTH)
AF:
0.0739
AC:
156
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
483
966
1449
1932
2415
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
112
224
336
448
560
<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:
0.0649
Hom.:
45
Bravo
AF:
0.0669
Asia WGS
AF:
0.0470
AC:
162
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
17
DANN
Benign
0.53
PhyloP100
0.99
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs62030374; hg19: chr15-76864453; API