chr15-76572112-C-T

Variant names:

• chr15-76572112-C-T
• rs62030374
• NM_020843.4:c.2838+2046G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.994
• Publications: 4 publications found

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

ACMG classification

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
SCAPER	NM_020843.4	c.2838+2046G>A		intron_variant	Intron 23 of 31	ENST00000563290.6	NP_065894.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCAPER	ENST00000563290.6	c.2838+2046G>A		intron_variant	Intron 23 of 31	5	NM_020843.4	ENSP00000454973.1

Frequencies

GnomAD3 genomes AF: 0.0670 AC: 10182 AN: 151990 Hom.: 381 Cov.: 32

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

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

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

Other links and lift over

dbSNP: rs62030374; hg19: chr15-76864453;