rs13182883

Variant names:

• chr5-137297649-G-A
• rs13182883
• NM_004598.4:c.187-30594C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-137297649-G-A
• chr5-137297649-G-C

Variant summary

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

The NM_004598.4(SPOCK1):​c.187-30594C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,772 control chromosomes in the GnomAD database, including 11,683 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 0.39 (11683 hom., cov: 31)
• Consequence: SPOCK1 NM_004598.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418
• Publications: 14 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=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPOCK1	NM_004598.4	c.187-30594C>T		intron_variant	Intron 2 of 10	ENST00000394945.6	NP_004589.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPOCK1	ENST00000394945.6	c.187-30594C>T		intron_variant	Intron 2 of 10	1	NM_004598.4	ENSP00000378401.1

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58542 AN: 151654 Hom.: 11667 Cov.: 31

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.386 AC: 58594 AN: 151772 Hom.: 11683 Cov.: 31 AF XY: 0.380 AC XY: 28222 AN XY: 74176

African (AFR) AF: 0.470 AC: 19429 AN: 41326

American (AMR) AF: 0.386 AC: 5898 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1366 AN: 3464

East Asian (EAS) AF: 0.449 AC: 2306 AN: 5138

South Asian (SAS) AF: 0.391 AC: 1874 AN: 4790

European-Finnish (FIN) AF: 0.268 AC: 2830 AN: 10556

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23723 AN: 67922

Other (OTH) AF: 0.399 AC: 840 AN: 2106

Alfa AF: 0.382 Hom.: 8866

Bravo AF: 0.397

Asia WGS AF: 0.383 AC: 1336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	2.4
DANN	Benign	0.90
PhyloP100		-0.42
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: rs13182883; hg19: chr5-136633338; COSMIC: COSV56442857;