rs1229708

Variant names:

• chr5-137363069-A-G
• rs1229708
• NM_004598.4:c.187-96014T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-137363069-A-G
• chr5-137363069-A-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.187-96014T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 152,034 control chromosomes in the GnomAD database, including 18,906 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 0.49 (18906 hom., cov: 32)
• Consequence: SPOCK1 NM_004598.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.851
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPOCK1	NM_004598.4	c.187-96014T>C		intron_variant	Intron 2 of 10	ENST00000394945.6	NP_004589.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPOCK1	ENST00000394945.6	c.187-96014T>C		intron_variant	Intron 2 of 10	1	NM_004598.4	ENSP00000378401.1

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74952 AN: 151916 Hom.: 18891 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.493 AC: 75002 AN: 152034 Hom.: 18906 Cov.: 32 AF XY: 0.492 AC XY: 36598 AN XY: 74316

African (AFR) AF: 0.415 AC: 17221 AN: 41454

American (AMR) AF: 0.554 AC: 8480 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1645 AN: 3466

East Asian (EAS) AF: 0.647 AC: 3342 AN: 5166

South Asian (SAS) AF: 0.636 AC: 3056 AN: 4802

European-Finnish (FIN) AF: 0.441 AC: 4662 AN: 10576

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34998 AN: 67958

Other (OTH) AF: 0.533 AC: 1125 AN: 2110

Alfa AF: 0.510 Hom.: 33756

Bravo AF: 0.495

Asia WGS AF: 0.630 AC: 2190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.70
DANN	Benign	0.34
PhyloP100		-0.85
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: rs1229708; hg19: chr5-136698758; COSMIC: COSV56443319;