rs17600115

chr5-137085263-G-Achr5-137085263-G-Cchr5-137085263-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004598.4(SPOCK1):c.475-17434C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,148 control chromosomes in the GnomAD database, including 1,633 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 0.13 (1633 hom., cov: 32)
• Consequence: SPOCK1 NM_004598.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPOCK1	NM_004598.4	c.475-17434C>T		intron_variant		ENST00000394945.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPOCK1	ENST00000394945.6	c.475-17434C>T		intron_variant		1	NM_004598.4	P1
SPOCK1	ENST00000510689.5	c.40-17434C>T		intron_variant		4
SPOCK1	ENST00000635347.1	n.448-17434C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19731 AN: 152030 Hom.: 1630 Cov.: 32

Gnomad AFR AF: 0.0334

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.130 AC: 19738 AN: 152148 Hom.: 1633 Cov.: 32 AF XY: 0.132 AC XY: 9791 AN XY: 74368

Gnomad4 AFR AF: 0.0333

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.121

Alfa AF: 0.102 Hom.: 210

Bravo AF: 0.123

Asia WGS AF: 0.146 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.3
Dann	Benign	0.52

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

Publications

LitVar

Other links and lift over

dbSNP: rs17600115; hg19: chr5-136420952;