rs11072511

Positions:

• chr15-74867092-A-G

Variant summary

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

The NM_005697.5(SCAMP2):​c.57+6107T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 152,054 control chromosomes in the GnomAD database, including 16,618 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 0.45 (16618 hom., cov: 33)
• Consequence: SCAMP2 NM_005697.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

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 (NFE) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCAMP2	NM_005697.5	c.57+6107T>C		intron_variant		ENST00000268099.13	NP_005688.2
SCAMP2	NM_001320778.2	c.57+6107T>C		intron_variant			NP_001307707.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCAMP2	ENST00000268099.13	c.57+6107T>C		intron_variant		1	NM_005697.5	ENSP00000268099	P1

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68916 AN: 151934 Hom.: 16599 Cov.: 33

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.454 AC: 68987 AN: 152054 Hom.: 16618 Cov.: 33 AF XY: 0.443 AC XY: 32943 AN XY: 74296

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.443

Alfa AF: 0.517 Hom.: 19908

Bravo AF: 0.461

Asia WGS AF: 0.245 AC: 856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.40

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: rs11072511; hg19: chr15-75159433;