rs1046188

Positions:

• chr1-155262283-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005698.4(SCAMP3):​c.-132G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 798,370 control chromosomes in the GnomAD database, including 43,589 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 0.36 (11367 hom., cov: 31)
  • Exomes 𝑓: 0.29 (32222 hom.)
• Consequence: SCAMP3 NM_005698.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCAMP3	NM_005698.4	c.-132G>A		5_prime_UTR_variant	1/9	ENST00000302631.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCAMP3	ENST00000302631.8	c.-132G>A		5_prime_UTR_variant	1/9	1	NM_005698.4	P1
SCAMP3	ENST00000355379.3	c.-132G>A		5_prime_UTR_variant	1/8	1
SCAMP3	ENST00000480219.1	n.47G>A		non_coding_transcript_exon_variant	1/2	2
SCAMP3	ENST00000497470.1	n.57G>A		non_coding_transcript_exon_variant	1/5	5

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54667 AN: 151902 Hom.: 11327 Cov.: 31

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.340

GnomAD4 exome AF: 0.290 AC: 187749 AN: 646350 Hom.: 32222 Cov.: 9 AF XY: 0.290 AC XY: 95663 AN XY: 330358

Gnomad4 AFR exome AF: 0.547

Gnomad4 AMR exome AF: 0.366

Gnomad4 ASJ exome AF: 0.229

Gnomad4 EAS exome AF: 0.728

Gnomad4 SAS exome AF: 0.318

Gnomad4 FIN exome AF: 0.280

Gnomad4 NFE exome AF: 0.247

Gnomad4 OTH exome AF: 0.301

GnomAD4 genome AF: 0.360 AC: 54758 AN: 152020 Hom.: 11367 Cov.: 31 AF XY: 0.362 AC XY: 26874 AN XY: 74300

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.336

Alfa AF: 0.281 Hom.: 6850

Bravo AF: 0.377

Asia WGS AF: 0.541 AC: 1884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.8
DANN	Benign	0.79

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1046188; hg19: chr1-155232074; COSMIC: COSV56944092; COSMIC: COSV56944092;