15-74844103-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCAMP2	NM_005697.5	c.*980G>A		3_prime_UTR_variant	Exon 9 of 9	ENST00000268099.13	NP_005688.2
SCAMP2	NM_001320778.2	c.*980G>A		3_prime_UTR_variant	Exon 10 of 10		NP_001307707.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCAMP2	ENST00000268099	c.*980G>A		3_prime_UTR_variant	Exon 9 of 9	1	NM_005697.5	ENSP00000268099.9
SCAMP2	ENST00000566480	c.*1268G>A		3_prime_UTR_variant	Exon 7 of 7	5		ENSP00000455377.1
SCAMP2	ENST00000563663.5	n.*1174G>A		non_coding_transcript_exon_variant	Exon 4 of 4	5		ENSP00000455963.1
SCAMP2	ENST00000563663.5	n.*1174G>A		3_prime_UTR_variant	Exon 4 of 4	5		ENSP00000455963.1

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.250

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.179

Gnomad4 OTH exome AF: 0.125

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

Gnomad4 AFR AF: 0.0733

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.572

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.210

Alfa AF: 0.136 Hom.: 323

Bravo AF: 0.170

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.5
DANN	Benign	0.56
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Publications

LitVar

Other links and lift over

dbSNP: rs872263; hg19: chr15-75136444;