rs1159929

chr5-78472997-G-Achr5-78472997-G-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCAMP1	NM_004866.6	c.853-2507G>A		intron_variant		ENST00000621999.5
SCAMP1	NM_001290229.2	c.775-2507G>A		intron_variant
SCAMP1	XM_011543727.4	c.751-2507G>A		intron_variant
SCAMP1	NR_110885.2	n.748-2507G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCAMP1	ENST00000621999.5	c.853-2507G>A		intron_variant		1	NM_004866.6	P1

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

Gnomad4 AFR AF: 0.908

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.754

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.857

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.811

Alfa AF: 0.780 Hom.: 7962

Bravo AF: 0.807

Asia WGS AF: 0.861 AC: 2995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.24
Dann	Benign	0.36

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: rs1159929; hg19: chr5-77768820;