chr5-78396793-T-A

Variant names:

• chr5-78396793-T-A
• rs2115436
• NM_004866.6:c.135+7879T>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.135+7879T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 152,138 control chromosomes in the GnomAD database, including 44,435 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 0.76 (44435 hom., cov: 32)
• Consequence: SCAMP1 NM_004866.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• Publications: 5 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=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCAMP1	NM_004866.6	c.135+7879T>A		intron_variant	Intron 2 of 8	ENST00000621999.5	NP_004857.4
SCAMP1	NM_001290229.2	c.58-18727T>A		intron_variant	Intron 1 of 7		NP_001277158.1
SCAMP1	NR_110885.2	n.190+7879T>A		intron_variant	Intron 2 of 7
SCAMP1	XM_011543727.4	c.135+7879T>A		intron_variant	Intron 2 of 7		XP_011542029.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCAMP1	ENST00000621999.5	c.135+7879T>A		intron_variant	Intron 2 of 8	1	NM_004866.6	ENSP00000481022.1

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115402 AN: 152020 Hom.: 44399 Cov.: 32

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.759 AC: 115487 AN: 152138 Hom.: 44435 Cov.: 32 AF XY: 0.755 AC XY: 56152 AN XY: 74370

African (AFR) AF: 0.836 AC: 34708 AN: 41496

American (AMR) AF: 0.598 AC: 9146 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2541 AN: 3472

East Asian (EAS) AF: 0.624 AC: 3234 AN: 5180

South Asian (SAS) AF: 0.766 AC: 3696 AN: 4826

European-Finnish (FIN) AF: 0.755 AC: 7996 AN: 10584

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.761 AC: 51755 AN: 67982

Other (OTH) AF: 0.763 AC: 1612 AN: 2114

Alfa AF: 0.758 Hom.: 5488

Bravo AF: 0.748

Asia WGS AF: 0.666 AC: 2319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	14
DANN	Benign	0.94
PhyloP100		0.26
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: rs2115436; hg19: chr5-77692617;