rs7170561

chr15-32676722-A-Cchr15-32676722-A-G

Variant summary

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

The NM_001144757.3(SCG5):c.227-3044A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 152,090 control chromosomes in the GnomAD database, including 11,634 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 0.38 (11634 hom., cov: 33)
• Consequence: SCG5 NM_001144757.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660

Genes affected

SCG5 (HGNC:10816): (secretogranin V) This gene encodes a secreted chaperone protein that prevents the aggregation of other secreted proteins, including proteins that are associated with neurodegenerative and metabolic disease. The encoded protein may be best known for its role in the trafficking and activation of prohormone convertase PC2 (encoded by Gene ID: 5126). Phosphorylation of the encoded protein has been shown to have an inhibitory effect on its chaperone function. This gene also produces a ARHGAP11A-SCG5 readthrough transcript and ARHGAP11A-SCG5 protein. [provided by RefSeq, Feb 2019]

ARHGAP11A-SCG5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCG5	NM_001144757.3	c.227-3044A>C		intron_variant		ENST00000300175.9
ARHGAP11A-SCG5	NM_001368319.1	c.1469-3044A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCG5	ENST00000300175.9	c.227-3044A>C		intron_variant		1	NM_001144757.3	P1

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58053 AN: 151972 Hom.: 11614 Cov.: 33

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.382 AC: 58118 AN: 152090 Hom.: 11634 Cov.: 33 AF XY: 0.388 AC XY: 28855 AN XY: 74358

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.379

Alfa AF: 0.334 Hom.: 11887

Bravo AF: 0.381

Asia WGS AF: 0.540 AC: 1872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.4
Dann	Benign	0.82

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: rs7170561; hg19: chr15-32968923;