NM_014978.3:c.1482+741C>G

Variant names:

• chr10-105148537-C-G
• rs10509785
• NM_014978.3:c.1482+741C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014978.3(SORCS3):​c.1482+741C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,014 control chromosomes in the GnomAD database, including 1,868 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 0.16 (1868 hom., cov: 32)
• Consequence: SORCS3 NM_014978.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797
• Publications: 2 publications found

Genes affected

SORCS3 (HGNC:16699): (sortilin related VPS10 domain containing receptor 3) This gene encodes a type-I receptor transmembrane protein that is a member of the vacuolar protein sorting 10 receptor family. Proteins of this family are defined by a vacuolar protein sorting 10 domain at the N-terminus. The N-terminal segment of this domain has a consensus motif for proprotein convertase processing, and the C-terminal segment of this domain is characterized by ten conserved cysteine residues. The vacuolar protein sorting 10 domain is followed by a leucine-rich segment, a transmembrane domain, and a short C-terminal cytoplasmic domain that interacts with adaptor molecules. The transcript is expressed at high levels in the brain, and candidate gene studies suggest that genetic variation in this gene is associated with Alzheimer's disease. Consistent with this observation, knockdown of the gene in cell culture results in an increase in amyloid precursor protein processing. [provided by RefSeq, Dec 2014]

SORCS3 Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SORCS3	NM_014978.3	c.1482+741C>G		intron_variant	Intron 9 of 26	ENST00000369701.8	NP_055793.1
SORCS3	XM_011539542.2	c.414+741C>G		intron_variant	Intron 5 of 22		XP_011537844.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SORCS3	ENST00000369701.8	c.1482+741C>G		intron_variant	Intron 9 of 26	1	NM_014978.3	ENSP00000358715.3

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23719 AN: 151896 Hom.: 1864 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.156 AC: 23746 AN: 152014 Hom.: 1868 Cov.: 32 AF XY: 0.157 AC XY: 11695 AN XY: 74338

African (AFR) AF: 0.153 AC: 6343 AN: 41472

American (AMR) AF: 0.190 AC: 2897 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3466

East Asian (EAS) AF: 0.171 AC: 882 AN: 5158

South Asian (SAS) AF: 0.223 AC: 1072 AN: 4812

European-Finnish (FIN) AF: 0.109 AC: 1160 AN: 10600

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10394 AN: 67938

Other (OTH) AF: 0.164 AC: 345 AN: 2104

Alfa AF: 0.162 Hom.: 268

Bravo AF: 0.163

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.8
DANN	Benign	0.65
PhyloP100		-0.80
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.16		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10509785; hg19: chr10-106908295;