chr15-74844103-C-T

Variant names:

• chr15-74844103-C-T
• rs872263
• NM_005697.5:c.*980G>A

Variant summary

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

The NM_005697.5(SCAMP2):​c.*980G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 151,434 control chromosomes in the GnomAD database, including 3,325 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 0.17 (3324 hom., cov: 29)
  • Exomes 𝑓: 0.17 (1 hom.)
• Consequence: SCAMP2 NM_005697.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202
• Publications: 13 publications found

Genes affected

SCAMP2 (HGNC:10564): (secretory carrier membrane protein 2) 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 the SCAMPs may function at the same site during vesicular transport rather than in separate pathways. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005697.5. 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
	SCAMP2	NM_005697.5	MANE Select	c.*980G>A		3_prime_UTR	Exon 9 of 9	NP_005688.2
	SCAMP2	NM_001320778.2		c.*980G>A		3_prime_UTR	Exon 10 of 10	NP_001307707.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCAMP2	ENST00000268099.13	TSL:1 MANE Select	c.*980G>A		3_prime_UTR	Exon 9 of 9	ENSP00000268099.9	O15127
	SCAMP2	ENST00000894365.1		c.*980G>A		3_prime_UTR	Exon 10 of 10	ENSP00000564424.1
	SCAMP2	ENST00000894366.1		c.*980G>A		3_prime_UTR	Exon 9 of 9	ENSP00000564425.1

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26257 AN: 151144 Hom.: 3324 Cov.: 29

Gnomad AFR AF: 0.0733

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.210

GnomAD4 exome AF: 0.169 AC: 30 AN: 178 Hom.: 1 Cov.: 0 AF XY: 0.184 AC XY: 25 AN XY: 136

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.179 AC: 28 AN: 156

Other (OTH) AF: 0.125 AC: 1 AN: 8

GnomAD4 genome AF: 0.174 AC: 26270 AN: 151256 Hom.: 3324 Cov.: 29 AF XY: 0.186 AC XY: 13732 AN XY: 73846

African (AFR) AF: 0.0733 AC: 3025 AN: 41248

American (AMR) AF: 0.284 AC: 4313 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 781 AN: 3460

East Asian (EAS) AF: 0.572 AC: 2907 AN: 5078

South Asian (SAS) AF: 0.474 AC: 2259 AN: 4764

European-Finnish (FIN) AF: 0.201 AC: 2107 AN: 10500

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10038 AN: 67722

Other (OTH) AF: 0.210 AC: 442 AN: 2100

Alfa AF: 0.119 Hom.: 382

Bravo AF: 0.170

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.5
DANN	Benign	0.56
PhyloP100		-0.20
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs872263; hg19: chr15-75136444;