chr15-75016309-C-T

Position:

• chr15-75016309-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138967.4(SCAMP5):​c.137-284C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,944 control chromosomes in the GnomAD database, including 25,908 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 0.53 (25908 hom., cov: 31)
• Consequence: SCAMP5 NM_138967.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560

Genes affected

SCAMP5 (HGNC:30386): (secretory carrier membrane protein 5) Involved in positive regulation of cytokine production; regulation of vesicle-mediated transport; and response to endoplasmic reticulum stress. Located in Golgi apparatus; plasma membrane; and recycling endosome membrane. Is integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SCAMP5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCAMP5	NM_138967.4	c.137-284C>T		intron_variant		ENST00000425597.8	NP_620417.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCAMP5	ENST00000425597.8	c.137-284C>T		intron_variant		1	NM_138967.4	ENSP00000406547.3

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80010 AN: 151826 Hom.: 25907 Cov.: 31

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.520

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.527 AC: 80025 AN: 151944 Hom.: 25908 Cov.: 31 AF XY: 0.521 AC XY: 38734 AN XY: 74276

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.712

Gnomad4 NFE AF: 0.736

Gnomad4 OTH AF: 0.519

Alfa AF: 0.688 Hom.: 59818

Bravo AF: 0.506

Asia WGS AF: 0.251 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.67
DANN	Benign	0.54

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: rs4886414; hg19: chr15-75308650; COSMIC: COSV62643613; COSMIC: COSV62643613;