rs6840362

Positions:

• chr4-87978768-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001040058.2(SPP1):​c.94-1278C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 151,976 control chromosomes in the GnomAD database, including 6,574 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 0.29 (6574 hom., cov: 31)
• Consequence: SPP1 NM_001040058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

Genes affected

SPP1 (HGNC:11255): (secreted phosphoprotein 1) The protein encoded by this gene is involved in the attachment of osteoclasts to the mineralized bone matrix. The encoded protein is secreted and binds hydroxyapatite with high affinity. The osteoclast vitronectin receptor is found in the cell membrane and may be involved in the binding to this protein. This protein is also a cytokine that upregulates expression of interferon-gamma and interleukin-12. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

SPP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPP1	NM_001040058.2	c.94-1278C>T		intron_variant		ENST00000395080.8	NP_001035147.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPP1	ENST00000395080.8	c.94-1278C>T		intron_variant		1	NM_001040058.2	ENSP00000378517.3

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43630 AN: 151860 Hom.: 6572 Cov.: 31

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.0462

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.287 AC: 43652 AN: 151976 Hom.: 6574 Cov.: 31 AF XY: 0.287 AC XY: 21295 AN XY: 74286

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.0465

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.250

Alfa AF: 0.298 Hom.: 3371

Bravo AF: 0.284

Asia WGS AF: 0.222 AC: 772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.67

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: rs6840362; hg19: chr4-88899920;