rs6884385

Positions:

• chr5-137517900-G-A
• chr5-137517900-G-C

Variant summary

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

The ENST00000503916.1(SPOCK1):​n.183-12193C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 151,976 control chromosomes in the GnomAD database, including 6,623 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 0.29 (6623 hom., cov: 32)
• Consequence: SPOCK1 ENST00000503916.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPOCK1	ENST00000503916.1	n.183-12193C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43577 AN: 151860 Hom.: 6625 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.287 AC: 43578 AN: 151976 Hom.: 6623 Cov.: 32 AF XY: 0.286 AC XY: 21263 AN XY: 74268

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.296

Alfa AF: 0.132 Hom.: 217

Bravo AF: 0.296

Asia WGS AF: 0.254 AC: 884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.6
DANN	Benign	0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6884385; hg19: chr5-136853589;