1-155260340-C-T

Position:

• chr1-155260340-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_005698.4(SCAMP3):​c.378G>A​(p.Gly126Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 1,611,504 control chromosomes in the GnomAD database, including 76,829 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 (11386 hom., cov: 32)
  • Exomes 𝑓: 0.28 (65443 hom.)
• Consequence: SCAMP3 NM_005698.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

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]

SCAMP3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BP7: Synonymous conserved (PhyloP=-1.24 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCAMP3	NM_005698.4	c.378G>A	p.Gly126Gly	synonymous_variant	4/9	ENST00000302631.8	NP_005689.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCAMP3	ENST00000302631.8	c.378G>A	p.Gly126Gly	synonymous_variant	4/9	1	NM_005698.4	ENSP00000307275.3

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54721 AN: 151892 Hom.: 11346 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.339

GnomAD3 exomes AF: 0.336 AC: 83946 AN: 250078 Hom.: 16425 AF XY: 0.323 AC XY: 43774 AN XY: 135318

Gnomad AFR exome AF: 0.551

Gnomad AMR exome AF: 0.408

Gnomad ASJ exome AF: 0.228

Gnomad EAS exome AF: 0.705

Gnomad SAS exome AF: 0.328

Gnomad FIN exome AF: 0.291

Gnomad NFE exome AF: 0.245

Gnomad OTH exome AF: 0.299

GnomAD4 exome AF: 0.284 AC: 414222 AN: 1459492 Hom.: 65443 Cov.: 36 AF XY: 0.282 AC XY: 204808 AN XY: 726184

Gnomad4 AFR exome AF: 0.546

Gnomad4 AMR exome AF: 0.402

Gnomad4 ASJ exome AF: 0.231

Gnomad4 EAS exome AF: 0.726

Gnomad4 SAS exome AF: 0.324

Gnomad4 FIN exome AF: 0.286

Gnomad4 NFE exome AF: 0.253

Gnomad4 OTH exome AF: 0.302

GnomAD4 genome AF: 0.361 AC: 54812 AN: 152012 Hom.: 11386 Cov.: 32 AF XY: 0.362 AC XY: 26913 AN XY: 74294

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.702

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.335

Alfa AF: 0.285 Hom.: 11536

Bravo AF: 0.377

Asia WGS AF: 0.543 AC: 1889 AN: 3478

EpiCase AF: 0.240

EpiControl AF: 0.232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	3.4
DANN	Benign	0.81
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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: rs1142287; hg19: chr1-155230131; COSMIC: COSV56944948; COSMIC: COSV56944948;