rs6872714

chr5-136984167-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPOCK1	NM_004598.4	c.991+973C>T		intron_variant		ENST00000394945.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPOCK1	ENST00000394945.6	c.991+973C>T		intron_variant		1	NM_004598.4	P1
SPOCK1	ENST00000509978.1	n.381+973C>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.391

Alfa AF: 0.402 Hom.: 21166

Bravo AF: 0.403

Asia WGS AF: 0.225 AC: 783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.4
Dann	Benign	0.68

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: rs6872714; hg19: chr5-136319856;