rs1008228480

Variant names:

• chr4-7192693-C-G
• rs1008228480
• NM_020777.3:c.47C>G

Your query was ambiguous. Multiple possible variants found:

• chr4-7192693-C-G
• chr4-7192693-C-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_020777.3(SORCS2):​c.47C>G​(p.Thr16Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 989,100 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T16P) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00048 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000043 (0 hom.)
• Consequence: SORCS2 NM_020777.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.01
• Publications: 0 publications found

Genes affected

SORCS2 (HGNC:16698): (sortilin related VPS10 domain containing receptor 2) This gene encodes one family member of vacuolar protein sorting 10 (VPS10) domain-containing receptor proteins. The VPS10 domain name comes from the yeast carboxypeptidase Y sorting receptor Vps10 protein. Members of this gene family are large with many exons but the CDS lengths are usually less than 3700 nt. Very large introns typically separate the exons encoding the VPS10 domain; the remaining exons are separated by much smaller-sized introns. These genes are strongly expressed in the central nervous system. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.046817422).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SORCS2	NM_020777.3	c.47C>G	p.Thr16Ser	missense_variant	Exon 1 of 27	ENST00000507866.6	NP_065828.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SORCS2	ENST00000507866.6	c.47C>G	p.Thr16Ser	missense_variant	Exon 1 of 27	1	NM_020777.3	ENSP00000422185.2

Frequencies

GnomAD3 genomes AF: 0.000491 AC: 72 AN: 146556 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00171

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000135

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000427 AC: 36 AN: 842440 Hom.: 0 Cov.: 29 AF XY: 0.0000333 AC XY: 13 AN XY: 390024

African (AFR) AF: 0.00207 AC: 33 AN: 15930

American (AMR) AF: 0.00 AC: 0 AN: 1324

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5344

East Asian (EAS) AF: 0.00 AC: 0 AN: 3896

South Asian (SAS) AF: 0.00 AC: 0 AN: 17372

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1178

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1644

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 767960

Other (OTH) AF: 0.000108 AC: 3 AN: 27792

GnomAD4 genome AF: 0.000484 AC: 71 AN: 146660 Hom.: 0 Cov.: 32 AF XY: 0.000378 AC XY: 27 AN XY: 71426

African (AFR) AF: 0.00168 AC: 69 AN: 40982

American (AMR) AF: 0.000135 AC: 2 AN: 14782

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3390

East Asian (EAS) AF: 0.00 AC: 0 AN: 5056

South Asian (SAS) AF: 0.00 AC: 0 AN: 4810

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8504

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 65892

Other (OTH) AF: 0.00 AC: 0 AN: 2042

Alfa AF: 0.000285 Hom.: 0

Bravo AF: 0.000506

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Feb 06, 2025

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.47C>G (p.T16S) alteration is located in exon 1 (coding exon 1) of the SORCS2 gene. This alteration results from a C to G substitution at nucleotide position 47, causing the threonine (T) at amino acid position 16 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.079
BayesDel_addAF	Benign	-0.66	T
BayesDel_noAF	Benign	-0.78
CADD	Benign	10
DANN	Benign	0.29
DEOGEN2	Benign	0.0037	T
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.062	N
LIST_S2	Benign	0.22	T
M_CAP	Benign	0.059	D
MetaRNN	Benign	0.047	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N
PhyloP100		1.0
PrimateAI	Uncertain	0.77	T
PROVEAN	Benign	-0.11	N
REVEL	Benign	0.033
Sift	Benign	0.26	T
Sift4G	Benign	0.86	T
Polyphen		0.0010	B
Vest4		0.076
MutPred		0.27		Loss of glycosylation at T16 (P = 0.028);
MVP		0.49
MPC		1.7
ClinPred		0.044	T
GERP RS		2.3
PromoterAI		-0.021	Neutral
Varity_R		0.045
gMVP		0.092
Mutation Taster		=93/7	polymorphism

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

Other links and lift over

dbSNP: rs1008228480; hg19: chr4-7194420;