chr5-137567007-G-A

Variant names:

• chr5-137567007-G-A
• rs1541364
• ENST00000503916.1:n.182+31191C>T

Variant summary

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

The ENST00000503916.1(SPOCK1):​n.182+31191C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 151,922 control chromosomes in the GnomAD database, including 17,303 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 0.47 (17303 hom., cov: 31)
• Consequence: SPOCK1 ENST00000503916.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• Publications: 5 publications found

Genes affected

SPOCK1 (HGNC:11251): (SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1) This gene encodes the protein core of a seminal plasma proteoglycan containing chondroitin- and heparan-sulfate chains. The protein's function is unknown, although similarity to thyropin-type cysteine protease-inhibitors suggests its function may be related to protease inhibition. [provided by RefSeq, Jul 2008]

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 (AMR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503916.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPOCK1	ENST00000503916.1	TSL:4	n.182+31191C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70937 AN: 151802 Hom.: 17300 Cov.: 31

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.467 AC: 70965 AN: 151922 Hom.: 17303 Cov.: 31 AF XY: 0.468 AC XY: 34762 AN XY: 74246

African (AFR) AF: 0.334 AC: 13843 AN: 41404

American (AMR) AF: 0.578 AC: 8827 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2237 AN: 3472

East Asian (EAS) AF: 0.536 AC: 2762 AN: 5156

South Asian (SAS) AF: 0.462 AC: 2222 AN: 4808

European-Finnish (FIN) AF: 0.463 AC: 4882 AN: 10542

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34558 AN: 67946

Other (OTH) AF: 0.506 AC: 1069 AN: 2112

Alfa AF: 0.500 Hom.: 41405

Bravo AF: 0.474

Asia WGS AF: 0.447 AC: 1558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.62
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1541364; hg19: chr5-136902696;