1-155262283-C-T

Variant names:

• chr1-155262283-C-T
• rs1046188
• NM_005698.4:c.-132G>A

Variant summary

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

The NM_005698.4(SCAMP3):​c.-132G>A variant causes a 5 prime UTR premature start codon gain 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_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 31 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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005698.4. 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
	SCAMP3	NM_005698.4	MANE Select	c.-132G>A		5_prime_UTR_premature_start_codon_gain	Exon 1 of 9	NP_005689.2
	SCAMP3	NM_005698.4	MANE Select	c.-132G>A		5_prime_UTR	Exon 1 of 9	NP_005689.2
	SCAMP3	NM_001438464.1		c.-132G>A		5_prime_UTR_premature_start_codon_gain	Exon 1 of 9	NP_001425393.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCAMP3	ENST00000302631.8	TSL:1 MANE Select	c.-132G>A		5_prime_UTR_premature_start_codon_gain	Exon 1 of 9	ENSP00000307275.3
	SCAMP3	ENST00000355379.3	TSL:1	c.-132G>A		5_prime_UTR_premature_start_codon_gain	Exon 1 of 8	ENSP00000347540.3
	SCAMP3	ENST00000302631.8	TSL:1 MANE Select	c.-132G>A		5_prime_UTR	Exon 1 of 9	ENSP00000307275.3

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

African (AFR) AF: 0.547 AC: 8781 AN: 16058

American (AMR) AF: 0.366 AC: 7042 AN: 19222

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 3462 AN: 15094

East Asian (EAS) AF: 0.728 AC: 22567 AN: 30998

South Asian (SAS) AF: 0.318 AC: 16369 AN: 51530

European-Finnish (FIN) AF: 0.280 AC: 8757 AN: 31282

Middle Eastern (MID) AF: 0.199 AC: 487 AN: 2450

European-Non Finnish (NFE) AF: 0.247 AC: 110564 AN: 447444

Other (OTH) AF: 0.301 AC: 9720 AN: 32272

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

African (AFR) AF: 0.541 AC: 22399 AN: 41434

American (AMR) AF: 0.334 AC: 5102 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 775 AN: 3464

East Asian (EAS) AF: 0.701 AC: 3617 AN: 5158

South Asian (SAS) AF: 0.337 AC: 1620 AN: 4814

European-Finnish (FIN) AF: 0.296 AC: 3132 AN: 10586

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17234 AN: 67962

Other (OTH) AF: 0.336 AC: 710 AN: 2116

Alfa AF: 0.305 Hom.: 11441

Bravo AF: 0.377

Asia WGS AF: 0.541 AC: 1884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.8
DANN	Benign	0.79
PhyloP100		-1.0
PromoterAI		-0.19	Neutral
Mutation Taster		=298/2	polymorphism (auto)

Splicing

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

Other links and lift over

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