rs17600115

Variant names:

• chr5-137085263-G-A
• rs17600115
• NM_004598.4:c.475-17434C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-137085263-G-A
• chr5-137085263-G-C
• chr5-137085263-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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]

ENSG00000299682 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004598.4. 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
	SPOCK1	NM_004598.4	MANE Select	c.475-17434C>T		intron	N/A	NP_004589.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPOCK1	ENST00000394945.6	TSL:1 MANE Select	c.475-17434C>T		intron	N/A	ENSP00000378401.1
	SPOCK1	ENST00000510689.5	TSL:4	c.40-17434C>T		intron	N/A	ENSP00000421677.1
	SPOCK1	ENST00000635347.1	TSL:5	n.448-17434C>T		intron	N/A

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

African (AFR) AF: 0.0333 AC: 1383 AN: 41550

American (AMR) AF: 0.187 AC: 2854 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3472

East Asian (EAS) AF: 0.123 AC: 633 AN: 5158

South Asian (SAS) AF: 0.148 AC: 712 AN: 4812

European-Finnish (FIN) AF: 0.207 AC: 2192 AN: 10568

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10977 AN: 67990

Other (OTH) AF: 0.121 AC: 256 AN: 2108

Alfa AF: 0.0996 Hom.: 210

Bravo AF: 0.123

Asia WGS AF: 0.146 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.3
DANN	Benign	0.52
PhyloP100		0.13
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: rs17600115; hg19: chr5-136420952;