rs1541364

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr5-137567007-G-A
• chr5-137567007-G-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPOCK1	ENST00000503916.1	n.182+31191C>T		intron_variant	Intron 1 of 4	4

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

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.506

Alfa AF: 0.514 Hom.: 27767

Bravo AF: 0.474

Asia WGS AF: 0.447 AC: 1558 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	2.7
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1541364; hg19: chr5-136902696;