5-137297649-G-A

Position:

• chr5-137297649-G-A

Variant summary

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

The ENST00000394945.6(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 ENST00000394945.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418

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=-0.73).
• 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/exons	MANE	Protein	UniProt
SPOCK1	NM_004598.4	c.187-30594C>T		intron_variant		ENST00000394945.6	NP_004589.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPOCK1	ENST00000394945.6	c.187-30594C>T		intron_variant		1	NM_004598.4	ENSP00000378401	P1

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

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.399

Alfa AF: 0.368 Hom.: 4714

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

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: rs13182883; hg19: chr5-136633338; COSMIC: COSV56442857;