chr5-137099794-G-T

Variant names:

• chr5-137099794-G-T
• rs7701979
• NM_004598.4:c.474+12641C>A

Variant summary

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

The NM_004598.4(SPOCK1):​c.474+12641C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 151,956 control chromosomes in the GnomAD database, including 5,282 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 0.25 (5282 hom., cov: 32)
• Consequence: SPOCK1 NM_004598.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537
• Publications: 4 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]

ENSG00000299682 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004598.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPOCK1	NM_004598.4	MANE Select	c.474+12641C>A		intron	N/A	NP_004589.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPOCK1	ENST00000394945.6	TSL:1 MANE Select	c.474+12641C>A		intron	N/A	ENSP00000378401.1
	SPOCK1	ENST00000510689.5	TSL:4	c.39+12641C>A		intron	N/A	ENSP00000421677.1
	SPOCK1	ENST00000635347.1	TSL:5	n.447+12641C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37775 AN: 151838 Hom.: 5276 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.249 AC: 37802 AN: 151956 Hom.: 5282 Cov.: 32 AF XY: 0.247 AC XY: 18319 AN XY: 74258

African (AFR) AF: 0.131 AC: 5417 AN: 41480

American (AMR) AF: 0.200 AC: 3060 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 873 AN: 3464

East Asian (EAS) AF: 0.147 AC: 758 AN: 5156

South Asian (SAS) AF: 0.292 AC: 1407 AN: 4812

European-Finnish (FIN) AF: 0.335 AC: 3520 AN: 10518

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21883 AN: 67948

Other (OTH) AF: 0.253 AC: 532 AN: 2104

Alfa AF: 0.296 Hom.: 29879

Bravo AF: 0.232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.66
DANN	Benign	0.49
PhyloP100		-0.54
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: rs7701979; hg19: chr5-136435483;