chr1-155262283-C-G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005698.4(SCAMP3):​c.-132G>C variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SCAMP3 NM_005698.4 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

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>C		5_prime_UTR_premature_start_codon_gain	Exon 1 of 9	NP_005689.2
	SCAMP3	NM_005698.4	MANE Select	c.-132G>C		5_prime_UTR	Exon 1 of 9	NP_005689.2
	SCAMP3	NM_001438464.1		c.-132G>C		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>C		5_prime_UTR_premature_start_codon_gain	Exon 1 of 9	ENSP00000307275.3
	SCAMP3	ENST00000355379.3	TSL:1	c.-132G>C		5_prime_UTR_premature_start_codon_gain	Exon 1 of 8	ENSP00000347540.3
	SCAMP3	ENST00000302631.8	TSL:1 MANE Select	c.-132G>C		5_prime_UTR	Exon 1 of 9	ENSP00000307275.3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 647512 Hom.: 0 Cov.: 9 AF XY: 0.00 AC XY: 0 AN XY: 330932

African (AFR) AF: 0.00 AC: 0 AN: 16088

American (AMR) AF: 0.00 AC: 0 AN: 19248

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15112

East Asian (EAS) AF: 0.00 AC: 0 AN: 31042

South Asian (SAS) AF: 0.00 AC: 0 AN: 51626

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31302

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2456

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 448314

Other (OTH) AF: 0.00 AC: 0 AN: 32324

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.5
DANN	Benign	0.43
PhyloP100		-1.0
PromoterAI		-0.025	Neutral

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;