rs1385513

Variant names:

• chr4-167229443-A-C
• rs1385513
• NM_001040159.2:c.189+4542T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-167229443-A-C
• chr4-167229443-A-T

Variant summary

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

The NM_001040159.2(SPOCK3):​c.189+4542T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 151,962 control chromosomes in the GnomAD database, including 4,854 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 0.23 (4854 hom., cov: 31)
• Consequence: SPOCK3 NM_001040159.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.05
• Publications: 3 publications found

Genes affected

SPOCK3 (HGNC:13565): (SPARC (osteonectin), cwcv and kazal like domains proteoglycan 3) This gene encodes a member of a novel family of calcium-binding proteoglycan proteins that contain thyroglobulin type-1 and Kazal-like domains. The encoded protein and may play a role in adult T-cell leukemia by inhibiting the activity of membrane-type matrix metalloproteinases. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPOCK3	NM_001040159.2	c.189+4542T>G		intron_variant	Intron 2 of 10	ENST00000357545.9	NP_001035249.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPOCK3	ENST00000357545.9	c.189+4542T>G		intron_variant	Intron 2 of 10	1	NM_001040159.2	ENSP00000350153.4

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35229 AN: 151842 Hom.: 4850 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.0911

Gnomad FIN AF: 0.0885

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.232 AC: 35271 AN: 151962 Hom.: 4854 Cov.: 31 AF XY: 0.228 AC XY: 16980 AN XY: 74314

African (AFR) AF: 0.383 AC: 15865 AN: 41386

American (AMR) AF: 0.290 AC: 4427 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3466

East Asian (EAS) AF: 0.205 AC: 1060 AN: 5164

South Asian (SAS) AF: 0.0893 AC: 431 AN: 4824

European-Finnish (FIN) AF: 0.0885 AC: 940 AN: 10618

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11353 AN: 67944

Other (OTH) AF: 0.248 AC: 523 AN: 2106

Alfa AF: 0.188 Hom.: 4720

Bravo AF: 0.259

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.3
DANN	Benign	0.66
PhyloP100		3.1
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: rs1385513; hg19: chr4-168150594;