chr10-106634912-T-C

Variant names:

• chr10-106634912-T-C
• rs4918245
• NM_052918.5:c.2476-5524A>G

Variant summary

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

The NM_052918.5(SORCS1):​c.2476-5524A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 152,132 control chromosomes in the GnomAD database, including 42,119 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 0.72 (42119 hom., cov: 32)
• Consequence: SORCS1 NM_052918.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 1 publications found

Genes affected

SORCS1 (HGNC:16697): (sortilin related VPS10 domain containing receptor 1) 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. Two of the five family members (sortilin and sortilin-related receptor) are synthesized as preproproteins; it is not yet known if this encoded protein is also a preproprotein. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

SORCS1 Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SORCS1	NM_052918.5	c.2476-5524A>G		intron_variant	Intron 18 of 25	ENST00000263054.11	NP_443150.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SORCS1	ENST00000263054.11	c.2476-5524A>G		intron_variant	Intron 18 of 25	1	NM_052918.5	ENSP00000263054.5
SORCS1	ENST00000369698.6	c.1207-5524A>G		intron_variant	Intron 10 of 18	5		ENSP00000358712.2

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109883 AN: 152014 Hom.: 42092 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.723 AC: 109951 AN: 152132 Hom.: 42119 Cov.: 32 AF XY: 0.722 AC XY: 53662 AN XY: 74362

African (AFR) AF: 0.460 AC: 19097 AN: 41484

American (AMR) AF: 0.825 AC: 12615 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.865 AC: 3002 AN: 3470

East Asian (EAS) AF: 0.484 AC: 2495 AN: 5158

South Asian (SAS) AF: 0.670 AC: 3221 AN: 4808

European-Finnish (FIN) AF: 0.851 AC: 9024 AN: 10598

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57814 AN: 67996

Other (OTH) AF: 0.772 AC: 1633 AN: 2114

Alfa AF: 0.788 Hom.: 6059

Bravo AF: 0.709

Asia WGS AF: 0.579 AC: 2015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	0.81
DANN	Benign	0.89
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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: rs4918245; hg19: chr10-108394670;