5-137162804-A-G

Position:

• chr5-137162804-A-G

Variant summary

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

The NM_004598.4(SPOCK1):​c.233-22110T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 152,060 control chromosomes in the GnomAD database, including 13,205 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 (13205 hom., cov: 33)
• Consequence: SPOCK1 NM_004598.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

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]

SPOCK1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPOCK1	NM_004598.4	c.233-22110T>C		intron_variant		ENST00000394945.6	NP_004589.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPOCK1	ENST00000394945.6	c.233-22110T>C		intron_variant		1	NM_004598.4	ENSP00000378401.1

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62494 AN: 151942 Hom.: 13193 Cov.: 33

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.411 AC: 62545 AN: 152060 Hom.: 13205 Cov.: 33 AF XY: 0.411 AC XY: 30577 AN XY: 74318

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.379

Alfa AF: 0.389 Hom.: 8357

Bravo AF: 0.419

Asia WGS AF: 0.449 AC: 1561 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.2
DANN	Benign	0.51

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: rs2043478; hg19: chr5-136498493; COSMIC: COSV56442296;