NM_004598.4:c.187-51850A>G

Variant names:

• chr5-137318905-T-C
• rs2950952
• NM_004598.4:c.187-51850A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004598.4(SPOCK1):​c.187-51850A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 152,234 control chromosomes in the GnomAD database, including 56,629 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 0.86 (56629 hom., cov: 32)
• Consequence: SPOCK1 NM_004598.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605
• Publications: 1 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPOCK1	NM_004598.4	c.187-51850A>G		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.187-51850A>G		intron_variant	Intron 2 of 10	1	NM_004598.4	ENSP00000378401.1

Frequencies

GnomAD3 genomes AF: 0.861 AC: 131005 AN: 152116 Hom.: 56568 Cov.: 32

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.898

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.861 AC: 131120 AN: 152234 Hom.: 56629 Cov.: 32 AF XY: 0.860 AC XY: 64038 AN XY: 74432

African (AFR) AF: 0.919 AC: 38183 AN: 41532

American (AMR) AF: 0.880 AC: 13474 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.898 AC: 3119 AN: 3472

East Asian (EAS) AF: 0.794 AC: 4110 AN: 5178

South Asian (SAS) AF: 0.755 AC: 3636 AN: 4818

European-Finnish (FIN) AF: 0.820 AC: 8697 AN: 10600

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57030 AN: 68014

Other (OTH) AF: 0.856 AC: 1808 AN: 2112

Alfa AF: 0.812 Hom.: 2482

Bravo AF: 0.871

Asia WGS AF: 0.747 AC: 2598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.2
DANN	Benign	0.67
PhyloP100		-0.60
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: rs2950952; hg19: chr5-136654594;