chr5-137380060-A-G

Position:

• chr5-137380060-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.187-113005T>C variant causes a intron change. The variant allele was found at a frequency of 0.298 in 152,064 control chromosomes in the GnomAD database, including 7,082 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 0.30 (7082 hom., cov: 32)
• Consequence: SPOCK1 NM_004598.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.85

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=-0.61).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPOCK1	NM_004598.4	c.187-113005T>C		intron_variant		ENST00000394945.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPOCK1	ENST00000394945.6	c.187-113005T>C		intron_variant		1	NM_004598.4	P1
SPOCK1	ENST00000505690.1	c.187-113005T>C		intron_variant		2
SPOCK1	ENST00000510689.5	c.-249-113005T>C		intron_variant		4
SPOCK1	ENST00000503916.1	n.252-113005T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45280 AN: 151946 Hom.: 7068 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.298 AC: 45308 AN: 152064 Hom.: 7082 Cov.: 32 AF XY: 0.302 AC XY: 22461 AN XY: 74350

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.340

Alfa AF: 0.322 Hom.: 16338

Bravo AF: 0.298

Asia WGS AF: 0.373 AC: 1295 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	16
DANN	Benign	0.79

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: rs1229742; hg19: chr5-136715749;