15-74867092-A-G

Variant names:

• chr15-74867092-A-G
• rs11072511
• NM_005697.5:c.57+6107T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005697.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCAMP2	NM_005697.5	MANE Select	c.57+6107T>C		intron	N/A	NP_005688.2
	SCAMP2	NM_001320778.2		c.57+6107T>C		intron	N/A	NP_001307707.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCAMP2	ENST00000268099.13	TSL:1 MANE Select	c.57+6107T>C		intron	N/A	ENSP00000268099.9
	SCAMP2	ENST00000564529.1	TSL:2	c.57+6107T>C		intron	N/A	ENSP00000457564.1
	SCAMP2	ENST00000562363.5	TSL:5	c.57+6107T>C		intron	N/A	ENSP00000457890.1

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

African (AFR) AF: 0.341 AC: 14132 AN: 41484

American (AMR) AF: 0.515 AC: 7873 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1587 AN: 3468

East Asian (EAS) AF: 0.265 AC: 1368 AN: 5166

South Asian (SAS) AF: 0.197 AC: 948 AN: 4816

European-Finnish (FIN) AF: 0.439 AC: 4632 AN: 10560

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36999 AN: 67964

Other (OTH) AF: 0.443 AC: 934 AN: 2106

Alfa AF: 0.513 Hom.: 25980

Bravo AF: 0.461

Asia WGS AF: 0.245 AC: 856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.40
PhyloP100		-1.3
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: rs11072511; hg19: chr15-75159433;