15-74863555-C-T

Variant names:

• chr15-74863555-C-T
• rs11630918
• NM_005697.5:c.58-8906G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SCAMP2	NM_005697.5	c.58-8906G>A		intron_variant	Intron 1 of 8	ENST00000268099.13	NP_005688.2
SCAMP2	NM_001320778.2	c.58-8906G>A		intron_variant	Intron 1 of 9		NP_001307707.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCAMP2	ENST00000268099.13	c.58-8906G>A		intron_variant	Intron 1 of 8	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

African (AFR) AF: 0.110 AC: 4546 AN: 41416

American (AMR) AF: 0.410 AC: 6235 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1379 AN: 3462

East Asian (EAS) AF: 0.159 AC: 818 AN: 5160

South Asian (SAS) AF: 0.124 AC: 594 AN: 4802

European-Finnish (FIN) AF: 0.406 AC: 4252 AN: 10468

Middle Eastern (MID) AF: 0.341 AC: 99 AN: 290

European-Non Finnish (NFE) AF: 0.525 AC: 35621 AN: 67856

Other (OTH) AF: 0.365 AC: 763 AN: 2092

Alfa AF: 0.465 Hom.: 22110

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
PhyloP100		-0.52
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: rs11630918; hg19: chr15-75155896;