5-78472997-G-A

Variant names:

• chr5-78472997-G-A
• rs1159929
• NM_004866.6:c.853-2507G>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.853-2507G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 152,064 control chromosomes in the GnomAD database, including 51,249 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 0.82 (51249 hom., cov: 32)
• Consequence: SCAMP1 NM_004866.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 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.853-2507G>A		intron	N/A	NP_004857.4
	SCAMP1	NM_001290229.2		c.775-2507G>A		intron	N/A	NP_001277158.1
	SCAMP1	NR_110885.2		n.748-2507G>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.853-2507G>A		intron	N/A	ENSP00000481022.1
	SCAMP1	ENST00000506858.2	TSL:1	n.278-2507G>A		intron	N/A
	SCAMP1	ENST00000614488.4	TSL:1	n.*219-2507G>A		intron	N/A	ENSP00000478071.1

Frequencies

GnomAD3 genomes AF: 0.816 AC: 123958 AN: 151946 Hom.: 51210 Cov.: 32

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.816 AC: 124044 AN: 152064 Hom.: 51249 Cov.: 32 AF XY: 0.813 AC XY: 60430 AN XY: 74348

African (AFR) AF: 0.908 AC: 37676 AN: 41516

American (AMR) AF: 0.654 AC: 9980 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2618 AN: 3472

East Asian (EAS) AF: 0.923 AC: 4774 AN: 5174

South Asian (SAS) AF: 0.857 AC: 4131 AN: 4820

European-Finnish (FIN) AF: 0.779 AC: 8241 AN: 10576

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54020 AN: 67930

Other (OTH) AF: 0.811 AC: 1713 AN: 2112

Alfa AF: 0.784 Hom.: 8280

Bravo AF: 0.807

Asia WGS AF: 0.861 AC: 2995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.36
PhyloP100		-0.24
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: rs1159929; hg19: chr5-77768820;