chr4-87978768-C-T

Variant names:

• chr4-87978768-C-T
• rs6840362
• NM_001040058.2:c.94-1278C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

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 Gene-Disease associations (from GenCC):

• systemic lupus erythematosus

  Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000286618 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040058.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPP1	NM_001040058.2	MANE Select	c.94-1278C>T		intron	N/A	NP_001035147.1
	SPP1	NM_001251830.2		c.132+918C>T		intron	N/A	NP_001238759.1
	SPP1	NM_000582.3		c.94-1278C>T		intron	N/A	NP_000573.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPP1	ENST00000395080.8	TSL:1 MANE Select	c.94-1278C>T		intron	N/A	ENSP00000378517.3
	SPP1	ENST00000237623.11	TSL:1	c.94-1278C>T		intron	N/A	ENSP00000237623.7
	SPP1	ENST00000360804.4	TSL:1	c.94-1625C>T		intron	N/A	ENSP00000354042.4

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

African (AFR) AF: 0.340 AC: 14094 AN: 41452

American (AMR) AF: 0.209 AC: 3184 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1113 AN: 3470

East Asian (EAS) AF: 0.0465 AC: 240 AN: 5158

South Asian (SAS) AF: 0.381 AC: 1836 AN: 4814

European-Finnish (FIN) AF: 0.255 AC: 2694 AN: 10550

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19525 AN: 67946

Other (OTH) AF: 0.250 AC: 527 AN: 2112

Alfa AF: 0.291 Hom.: 12374

Bravo AF: 0.284

Asia WGS AF: 0.222 AC: 772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.67
PhyloP100		0.23
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: rs6840362; hg19: chr4-88899920;