1-155260340-C-T

Variant names:

• chr1-155260340-C-T
• rs1142287
• NM_005698.4:c.378G>A

Variant summary

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

The NM_001438473.1(SCAMP3):​c.14G>A​(p.Gly5Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 1,611,504 control chromosomes in the GnomAD database, including 76,829 homozygotes. In-silico tool predicts a benign outcome for this variant. 5/6 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.36 (11386 hom., cov: 32)
  • Exomes 𝑓: 0.28 (65443 hom.)
• Consequence: SCAMP3 NM_001438473.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 42 publications found

Genes affected

SCAMP3 (HGNC:10565): (secretory carrier membrane protein 3) This gene encodes an integral membrane protein that belongs to the secretory carrier membrane protein family. The encoded protein functions as a carrier to the cell surface in post-golgi recycling pathways. This protein is also involved in protein trafficking in endosomal pathways. Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2011]

ENSG00000303088 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001438473.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCAMP3	NM_005698.4	MANE Select	c.378G>A	p.Gly126Gly	synonymous	Exon 4 of 9	NP_005689.2
	SCAMP3	NM_001438473.1		c.14G>A	p.Gly5Glu	missense	Exon 4 of 9	NP_001425402.1
	SCAMP3	NM_001438464.1		c.378G>A	p.Gly126Gly	synonymous	Exon 4 of 9	NP_001425393.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCAMP3	ENST00000302631.8	TSL:1 MANE Select	c.378G>A	p.Gly126Gly	synonymous	Exon 4 of 9	ENSP00000307275.3	O14828-1
	SCAMP3	ENST00000355379.3	TSL:1	c.300G>A	p.Gly100Gly	synonymous	Exon 3 of 8	ENSP00000347540.3	O14828-2
	SCAMP3	ENST00000880568.1		c.378G>A	p.Gly126Gly	synonymous	Exon 4 of 9	ENSP00000550627.1

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54721 AN: 151892 Hom.: 11346 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.339

GnomAD2 exomes AF: 0.336 AC: 83946 AN: 250078 AF XY: 0.323

Gnomad AFR exome AF: 0.551

Gnomad AMR exome AF: 0.408

Gnomad ASJ exome AF: 0.228

Gnomad EAS exome AF: 0.705

Gnomad FIN exome AF: 0.291

Gnomad NFE exome AF: 0.245

Gnomad OTH exome AF: 0.299

GnomAD4 exome AF: 0.284 AC: 414222 AN: 1459492 Hom.: 65443 Cov.: 36 AF XY: 0.282 AC XY: 204808 AN XY: 726184

African (AFR) AF: 0.546 AC: 18268 AN: 33478

American (AMR) AF: 0.402 AC: 17999 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 6044 AN: 26134

East Asian (EAS) AF: 0.726 AC: 28801 AN: 39698

South Asian (SAS) AF: 0.324 AC: 27942 AN: 86256

European-Finnish (FIN) AF: 0.286 AC: 14621 AN: 51136

Middle Eastern (MID) AF: 0.201 AC: 1161 AN: 5762

European-Non Finnish (NFE) AF: 0.253 AC: 281126 AN: 1111932

Other (OTH) AF: 0.302 AC: 18260 AN: 60372

GnomAD4 genome AF: 0.361 AC: 54812 AN: 152012 Hom.: 11386 Cov.: 32 AF XY: 0.362 AC XY: 26913 AN XY: 74294

African (AFR) AF: 0.541 AC: 22431 AN: 41456

American (AMR) AF: 0.334 AC: 5110 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 775 AN: 3472

East Asian (EAS) AF: 0.702 AC: 3622 AN: 5162

South Asian (SAS) AF: 0.338 AC: 1625 AN: 4814

European-Finnish (FIN) AF: 0.296 AC: 3123 AN: 10548

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17254 AN: 67960

Other (OTH) AF: 0.335 AC: 704 AN: 2104

Alfa AF: 0.298 Hom.: 27608

Bravo AF: 0.377

Asia WGS AF: 0.543 AC: 1889 AN: 3478

EpiCase AF: 0.240

EpiControl AF: 0.232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	3.4
DANN	Benign	0.81
PhyloP100		-1.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
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: rs1142287; hg19: chr1-155230131; COSMIC: COSV56944948; COSMIC: COSV56944948;