rs7097380

Variant names:

• chr10-106921911-G-A
• rs7097380
• NM_052918.5:c.626+34602C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-106921911-G-A
• chr10-106921911-G-C
• chr10-106921911-G-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000263054.11(SORCS1):​c.626+34602C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,974 control chromosomes in the GnomAD database, including 7,868 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 0.32 (7868 hom., cov: 33)
• Consequence: SORCS1 ENST00000263054.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 4 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000263054.11. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SORCS1	NM_052918.5	MANE Select	c.626+34602C>T		intron	N/A	NP_443150.3
	SORCS1	NM_001387556.1		c.626+34602C>T		intron	N/A	NP_001374485.1
	SORCS1	NM_001013031.3		c.626+34602C>T		intron	N/A	NP_001013049.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SORCS1	ENST00000263054.11	TSL:1 MANE Select	c.626+34602C>T		intron	N/A	ENSP00000263054.5

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47902 AN: 151856 Hom.: 7872 Cov.: 33

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.315 AC: 47912 AN: 151974 Hom.: 7868 Cov.: 33 AF XY: 0.313 AC XY: 23217 AN XY: 74276

African (AFR) AF: 0.259 AC: 10733 AN: 41434

American (AMR) AF: 0.314 AC: 4794 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1446 AN: 3468

East Asian (EAS) AF: 0.144 AC: 743 AN: 5170

South Asian (SAS) AF: 0.268 AC: 1290 AN: 4812

European-Finnish (FIN) AF: 0.302 AC: 3182 AN: 10534

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24776 AN: 67970

Other (OTH) AF: 0.322 AC: 679 AN: 2110

Alfa AF: 0.345 Hom.: 41133

Bravo AF: 0.310

Asia WGS AF: 0.212 AC: 739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	12
DANN	Benign	0.66
PhyloP100		1.1
Mutation Taster		=99/1	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: rs7097380; hg19: chr10-108681669;