XM_047416477.1:c.-880G>T

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The XM_047416477.1(LOC124900647):​c.-880G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000987 in 152,014 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000099 (0 hom., cov: 33)
• Consequence: LOC124900647 XM_047416477.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492

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

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900647	XM_047416477.1	c.-880G>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 2 of 3		XP_047272433.1
LOC124900647	XM_047416478.1	c.-880G>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 5		XP_047272434.1
LOC124900647	XM_047416477.1	c.-880G>T		5_prime_UTR_variant	Exon 2 of 3		XP_047272433.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0000987 AC: 15 AN: 152014 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000362

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000987 AC: 15 AN: 152014 Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9 AN XY: 74248

Gnomad4 AFR AF: 0.000362

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

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	0.45

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: rs11247978; hg19: chr4-1186494;