NM_006108.4:c.677-17280G>A

Variant names:

• chr11-14118140-G-A
• rs1528648
• NM_006108.4:c.677-17280G>A

Variant summary

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

The NM_006108.4(SPON1):​c.677-17280G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.763 in 152,164 control chromosomes in the GnomAD database, including 44,876 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 0.76 (44876 hom., cov: 32)
• Consequence: SPON1 NM_006108.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.399
• Publications: 2 publications found

Genes affected

SPON1 (HGNC:11252): (spondin 1) Predicted to be an extracellular matrix structural constituent. Predicted to be involved in cell adhesion. Predicted to act upstream of or within positive regulation of protein binding activity; positive regulation of protein processing; and regulation of amyloid precursor protein catabolic process. Located in extracellular space. Colocalizes with collagen-containing extracellular matrix. [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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPON1	NM_006108.4	c.677-17280G>A		intron_variant	Intron 5 of 15	ENST00000576479.4	NP_006099.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPON1	ENST00000576479.4	c.677-17280G>A		intron_variant	Intron 5 of 15	1	NM_006108.4	ENSP00000460236.1

Frequencies

GnomAD3 genomes AF: 0.763 AC: 116063 AN: 152046 Hom.: 44825 Cov.: 32

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.763 AC: 116172 AN: 152164 Hom.: 44876 Cov.: 32 AF XY: 0.767 AC XY: 57045 AN XY: 74382

African (AFR) AF: 0.880 AC: 36541 AN: 41524

American (AMR) AF: 0.778 AC: 11890 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 2805 AN: 3466

East Asian (EAS) AF: 0.818 AC: 4238 AN: 5184

South Asian (SAS) AF: 0.742 AC: 3582 AN: 4826

European-Finnish (FIN) AF: 0.750 AC: 7931 AN: 10580

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46798 AN: 67982

Other (OTH) AF: 0.757 AC: 1598 AN: 2110

Alfa AF: 0.714 Hom.: 19032

Bravo AF: 0.770

Asia WGS AF: 0.794 AC: 2761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.5
DANN	Benign	0.43
PhyloP100		0.40

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: rs1528648; hg19: chr11-14139686;