rs1869959

Positions:

• chr15-74854991-A-C
• chr15-74854991-A-G
• chr15-74854991-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005697.5(SCAMP2):​c.58-342T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 144,702 control chromosomes in the GnomAD database, including 33,202 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 0.68 (33202 hom., cov: 24)
• Consequence: SCAMP2 NM_005697.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09

Genes affected

SCAMP2 (HGNC:10564): (secretory carrier membrane protein 2) This gene product belongs to the SCAMP family of proteins which are secretory carrier membrane proteins. They function as carriers to the cell surface in post-golgi recycling pathways. Different family members are highly related products of distinct genes, and are usually expressed together. These findings suggest that the SCAMPs may function at the same site during vesicular transport rather than in separate pathways. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCAMP2	NM_005697.5	c.58-342T>G		intron_variant		ENST00000268099.13	NP_005688.2
SCAMP2	NM_001320778.2	c.58-342T>G		intron_variant			NP_001307707.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCAMP2	ENST00000268099.13	c.58-342T>G		intron_variant		1	NM_005697.5	ENSP00000268099	P1

Frequencies

GnomAD3 genomes AF: 0.682 AC: 98667 AN: 144644 Hom.: 33190 Cov.: 24

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.723

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.674

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.682 AC: 98705 AN: 144702 Hom.: 33202 Cov.: 24 AF XY: 0.681 AC XY: 47794 AN XY: 70138

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.692

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.674

Alfa AF: 0.464 Hom.: 621

Bravo AF: 0.669

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.066
DANN	Benign	0.33

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

LitVar

Other links and lift over

dbSNP: rs1869959; hg19: chr15-75147332;