rs10065260

Variant names:

• chr5-78367612-C-A
• rs10065260
• NM_004866.6:c.57+6884C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004866.6(SCAMP1):​c.57+6884C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 152,120 control chromosomes in the GnomAD database, including 16,025 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 (16025 hom., cov: 32)
• Consequence: SCAMP1 NM_004866.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 6 publications found

Genes affected

SCAMP1 (HGNC:10563): (secretory carrier membrane protein 1) 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 these protein family members may function at the same site during vesicular transport rather than in separate pathways. A pseudogene of this gene has been defined on chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004866.6. 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
	SCAMP1	NM_004866.6	MANE Select	c.57+6884C>A		intron	N/A	NP_004857.4
	SCAMP1	NM_001290229.2		c.57+6884C>A		intron	N/A	NP_001277158.1
	SCAMP1	NR_110885.2		n.112+6884C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCAMP1	ENST00000621999.5	TSL:1 MANE Select	c.57+6884C>A		intron	N/A	ENSP00000481022.1
	SCAMP1	ENST00000614488.4	TSL:1	n.57+6884C>A		intron	N/A	ENSP00000478071.1
	SCAMP1	ENST00000618166.4	TSL:2	c.57+6884C>A		intron	N/A	ENSP00000480865.1

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67962 AN: 152002 Hom.: 16006 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.0851

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.447 AC: 68034 AN: 152120 Hom.: 16025 Cov.: 32 AF XY: 0.441 AC XY: 32792 AN XY: 74360

African (AFR) AF: 0.420 AC: 17443 AN: 41488

American (AMR) AF: 0.373 AC: 5701 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1675 AN: 3470

East Asian (EAS) AF: 0.0853 AC: 442 AN: 5182

South Asian (SAS) AF: 0.353 AC: 1699 AN: 4818

European-Finnish (FIN) AF: 0.518 AC: 5468 AN: 10566

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34176 AN: 67990

Other (OTH) AF: 0.446 AC: 940 AN: 2106

Alfa AF: 0.459 Hom.: 7509

Bravo AF: 0.434

Asia WGS AF: 0.218 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.75
PhyloP100		-0.29
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: rs10065260; hg19: chr5-77663436;