15-76404427-T-A

Variant names:

• chr15-76404427-T-A
• rs3743175
• NM_020843.4:c.3467+97A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B.

Score: -2 - Likely Benign

-2

PM2BP4_Strong

The NM_020843.4(SCAPER):​c.3467+97A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SCAPER NM_020843.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 18 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCAPER	NM_020843.4	c.3467+97A>T		intron_variant	Intron 27 of 31	ENST00000563290.6	NP_065894.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCAPER	ENST00000563290.6	c.3467+97A>T		intron_variant	Intron 27 of 31	5	NM_020843.4	ENSP00000454973.1
SCAPER	ENST00000324767.11	c.3467+97A>T		intron_variant	Intron 26 of 30	1		ENSP00000326924.7
SCAPER	ENST00000538941.6	c.2729+97A>T		intron_variant	Intron 27 of 31	1		ENSP00000442190.2
SCAPER	ENST00000303521.10	n.3531+97A>T		intron_variant	Intron 26 of 26	2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1058052 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 522610

African (AFR) AF: 0.00 AC: 0 AN: 24108

American (AMR) AF: 0.00 AC: 0 AN: 25868

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16900

East Asian (EAS) AF: 0.00 AC: 0 AN: 34418

South Asian (SAS) AF: 0.00 AC: 0 AN: 47710

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34188

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4580

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 825198

Other (OTH) AF: 0.00 AC: 0 AN: 45082

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 816

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	0.65
DANN	Benign	0.87
PhyloP100		-1.3

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: rs3743175; hg19: chr15-76696768;