XM_047416477.1:c.-880G>C

Variant names:

• chr4-1192706-G-C
• rs11247978
• XM_047416477.1:c.-880G>C

Variant summary

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

The XM_047416477.1(LOC124900647):​c.-880G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 152,092 control chromosomes in the GnomAD database, including 11,279 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 0.36 (11279 hom., cov: 33)
• Consequence: LOC124900647 XM_047416477.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492
• Publications: 2 publications found

Genes affected

LOC124900647 (HGNC:):

SPON2 (HGNC:11253): (spondin 2) Predicted to enable antigen binding activity; lipopolysaccharide binding activity; and metal ion binding activity. Predicted to be involved in cell adhesion. Predicted to act upstream of or within several processes, including defense response to other organism; opsonization; and positive regulation of cytokine production. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900647	XM_047416477.1	c.-880G>C		5_prime_UTR_variant	Exon 2 of 3		XP_047272433.1
LOC124900647	XM_047416478.1	c.-880G>C		5_prime_UTR_variant	Exon 1 of 5		XP_047272434.1
SPON2	NM_001199021.2	c.-238-13165C>G		intron_variant	Intron 1 of 7		NP_001185950.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPON2	ENST00000617421.4	c.-238-13165C>G		intron_variant	Intron 1 of 7	5		ENSP00000483599.1
SPON2	ENST00000515004.5	c.-234+2284C>G		intron_variant	Intron 1 of 3	4		ENSP00000425871.1
SPON2	ENST00000502483.5	c.-239+2284C>G		intron_variant	Intron 1 of 3	4		ENSP00000422516.1

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54794 AN: 151974 Hom.: 11281 Cov.: 33

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.360 AC: 54795 AN: 152092 Hom.: 11279 Cov.: 33 AF XY: 0.361 AC XY: 26820 AN XY: 74360

African (AFR) AF: 0.168 AC: 6986 AN: 41490

American (AMR) AF: 0.356 AC: 5437 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1436 AN: 3472

East Asian (EAS) AF: 0.177 AC: 918 AN: 5176

South Asian (SAS) AF: 0.369 AC: 1780 AN: 4824

European-Finnish (FIN) AF: 0.521 AC: 5518 AN: 10582

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31422 AN: 67952

Other (OTH) AF: 0.335 AC: 708 AN: 2112

Alfa AF: 0.296 Hom.: 902

Bravo AF: 0.334

Asia WGS AF: 0.245 AC: 855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.40
PhyloP100		-0.49

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: rs11247978; hg19: chr4-1186494; COSMIC: COSV72202179; COSMIC: COSV72202179;