15-74863555-C-T

Position:

• chr15-74863555-C-T

Variant summary

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

The NM_005697.5(SCAMP2):​c.58-8906G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,666 control chromosomes in the GnomAD database, including 12,483 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 0.36 (12483 hom., cov: 30)
• Consequence: SCAMP2 NM_005697.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.521

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]

SCAMP2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCAMP2	NM_005697.5	c.58-8906G>A		intron_variant		ENST00000268099.13	NP_005688.2
SCAMP2	NM_001320778.2	c.58-8906G>A		intron_variant			NP_001307707.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCAMP2	ENST00000268099.13	c.58-8906G>A		intron_variant		1	NM_005697.5	ENSP00000268099.9

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54652 AN: 151550 Hom.: 12484 Cov.: 30

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.340

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.360 AC: 54657 AN: 151666 Hom.: 12483 Cov.: 30 AF XY: 0.349 AC XY: 25831 AN XY: 74078

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.365

Alfa AF: 0.477 Hom.: 17408

Bravo AF: 0.357

Asia WGS AF: 0.141 AC: 495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.50

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: rs11630918; hg19: chr15-75155896;