Variant 15-32679733-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001144757.3(SCG5):c.227-33C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 1,606,720 control chromosomes in the GnomAD database, including 56,014 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.26 ( 5554 hom., cov: 32)

Exomes 𝑓: 0.25 ( 50460 hom. )

Consequence

SCG5
NM_001144757.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0700

Variant links:

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]

SCG5 links:

ARHGAP11A-SCG5 (HGNC:):

ARHGAP11A-SCG5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 15-32679733-C-T is Benign according to our data. Variant chr15-32679733-C-T is described in ClinVar as [Benign]. Clinvar id is 1239157.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCG5	NM_001144757.3 linkuse as main transcript	c.227-33C>T		intron_variant		ENST00000300175.9
ARHGAP11A-SCG5	NM_001368319.1 linkuse as main transcript	c.1469-33C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCG5	ENST00000300175.9 linkuse as main transcript	c.227-33C>T		intron_variant		1	NM_001144757.3	P1	P05408-1

Frequencies

GnomAD3 genomes

AF:

0.257

AC:

39083

AN:

151948

Hom.:

5552

Cov.:

show subpopulations

Gnomad AFR

AF:

0.219

Gnomad AMI

AF:

0.216

Gnomad AMR

AF:

0.282

Gnomad ASJ

AF:

0.189

Gnomad EAS

AF:

0.592

Gnomad SAS

AF:

0.422

Gnomad FIN

AF:

0.366

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.225

Gnomad OTH

AF:

0.260

GnomAD3 exomes

AF:

0.299

AC:

74352

AN:

248296

Hom.:

12705

AF XY:

0.301

AC XY:

40584

AN XY:

134672

show subpopulations

Gnomad AFR exome

AF:

0.217

Gnomad AMR exome

AF:

0.317

Gnomad ASJ exome

AF:

0.194

Gnomad EAS exome

AF:

0.587

Gnomad SAS exome

AF:

0.412

Gnomad FIN exome

AF:

0.371

Gnomad NFE exome

AF:

0.226

Gnomad OTH exome

AF:

0.280

GnomAD4 exome

AF:

0.249

AC:

362631

AN:

1454654

Hom.:

50460

Cov.:

AF XY:

0.254

AC XY:

183623

AN XY:

723890

show subpopulations

Gnomad4 AFR exome

AF:

0.214

Gnomad4 AMR exome

AF:

0.312

Gnomad4 ASJ exome

AF:

0.191

Gnomad4 EAS exome

AF:

0.589

Gnomad4 SAS exome

AF:

0.403

Gnomad4 FIN exome

AF:

0.369

Gnomad4 NFE exome

AF:

0.218

Gnomad4 OTH exome

AF:

0.267

GnomAD4 genome

AF:

0.257

AC:

39102

AN:

152066

Hom.:

5554

Cov.:

AF XY:

0.269

AC XY:

19990

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.219

Gnomad4 AMR

AF:

0.282

Gnomad4 ASJ

AF:

0.189

Gnomad4 EAS

AF:

0.592

Gnomad4 SAS

AF:

0.421

Gnomad4 FIN

AF:

0.366

Gnomad4 NFE

AF:

0.225

Gnomad4 OTH

AF:

0.260

Alfa

AF:

0.230

Hom.:

7385

Bravo

AF:

0.245

Asia WGS

AF:

0.486

AC:

1687

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

Cadd

Benign

7.3

Dann

Benign

0.73

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over