rs6872714

Variant names:

• chr5-136984167-G-A
• rs6872714
• NM_004598.4:c.991+973C>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.991+973C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 152,020 control chromosomes in the GnomAD database, including 13,420 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 0.41 (13420 hom., cov: 32)
• Consequence: SPOCK1 NM_004598.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPOCK1	NM_004598.4	MANE Select	c.991+973C>T		intron	N/A	NP_004589.1	Q08629

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPOCK1	ENST00000394945.6	TSL:1 MANE Select	c.991+973C>T		intron	N/A	ENSP00000378401.1	Q08629
	SPOCK1	ENST00000509978.1	TSL:4	n.381+973C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62521 AN: 151902 Hom.: 13391 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.412 AC: 62598 AN: 152020 Hom.: 13420 Cov.: 32 AF XY: 0.409 AC XY: 30402 AN XY: 74308

African (AFR) AF: 0.472 AC: 19588 AN: 41462

American (AMR) AF: 0.362 AC: 5528 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1234 AN: 3470

East Asian (EAS) AF: 0.130 AC: 673 AN: 5188

South Asian (SAS) AF: 0.240 AC: 1156 AN: 4816

European-Finnish (FIN) AF: 0.496 AC: 5229 AN: 10550

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27884 AN: 67934

Other (OTH) AF: 0.391 AC: 826 AN: 2112

Alfa AF: 0.405 Hom.: 49053

Bravo AF: 0.403

Asia WGS AF: 0.225 AC: 783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.4
DANN	Benign	0.68
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: rs6872714; hg19: chr5-136319856;