rs2005698

Variant names:

• chr5-137391062-C-A
• rs2005698
• NM_004598.4:c.186+107311G>T

Your query was ambiguous. Multiple possible variants found:

• chr5-137391062-C-A
• chr5-137391062-C-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.186+107311G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,782 control chromosomes in the GnomAD database, including 8,198 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 0.33 (8198 hom., cov: 31)
• Consequence: SPOCK1 NM_004598.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 0 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPOCK1	NM_004598.4	c.186+107311G>T		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.186+107311G>T		intron_variant	Intron 2 of 10	1	NM_004598.4	ENSP00000378401.1
SPOCK1	ENST00000505690.1	c.186+107311G>T		intron_variant	Intron 1 of 3	2		ENSP00000424517.1
SPOCK1	ENST00000510689.5	c.-250+108117G>T		intron_variant	Intron 1 of 5	4		ENSP00000421677.1
SPOCK1	ENST00000503916.1	n.251+114577G>T		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49616 AN: 151664 Hom.: 8173 Cov.: 31

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.327 AC: 49673 AN: 151782 Hom.: 8198 Cov.: 31 AF XY: 0.330 AC XY: 24486 AN XY: 74186

African (AFR) AF: 0.297 AC: 12283 AN: 41342

American (AMR) AF: 0.428 AC: 6529 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1093 AN: 3466

East Asian (EAS) AF: 0.298 AC: 1527 AN: 5132

South Asian (SAS) AF: 0.393 AC: 1885 AN: 4796

European-Finnish (FIN) AF: 0.327 AC: 3442 AN: 10532

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21906 AN: 67930

Other (OTH) AF: 0.365 AC: 771 AN: 2110

Alfa AF: 0.297 Hom.: 2783

Bravo AF: 0.333

Asia WGS AF: 0.390 AC: 1353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.095
DANN	Benign	0.34
PhyloP100		-1.9
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: rs2005698; hg19: chr5-136726751;