8-73095112-G-T

Variant names:

• chr8-73095112-G-T
• rs12677663
• ENST00000519697.1:n.583-13899C>A

Variant summary

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

The ENST00000519697.1(SBSPON):​n.583-13899C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 151,514 control chromosomes in the GnomAD database, including 32,607 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 0.65 (32607 hom., cov: 28)
• Consequence: SBSPON ENST00000519697.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 24 publications found

Genes affected

SBSPON (HGNC:30362): (somatomedin B and thrombospondin type 1 domain containing) Predicted to be an extracellular matrix structural constituent. 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519697.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SBSPON	ENST00000519697.1	TSL:2	n.583-13899C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98416 AN: 151396 Hom.: 32551 Cov.: 28

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.650 AC: 98532 AN: 151514 Hom.: 32607 Cov.: 28 AF XY: 0.653 AC XY: 48299 AN XY: 73970

African (AFR) AF: 0.779 AC: 32178 AN: 41332

American (AMR) AF: 0.597 AC: 9073 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2267 AN: 3464

East Asian (EAS) AF: 0.837 AC: 4304 AN: 5144

South Asian (SAS) AF: 0.676 AC: 3213 AN: 4754

European-Finnish (FIN) AF: 0.572 AC: 5992 AN: 10468

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39342 AN: 67858

Other (OTH) AF: 0.673 AC: 1412 AN: 2098

Alfa AF: 0.607 Hom.: 111730

Bravo AF: 0.657

Asia WGS AF: 0.756 AC: 2630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.58
DANN	Benign	0.46
PhyloP100		-0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12677663; hg19: chr8-74007347;