rs12677663

chr8-73095112-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000519697.1(SBSPON):n.583-13899C>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SBSPON	ENST00000519697.1	n.583-13899C>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.837

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.673

Alfa AF: 0.600 Hom.: 47953

Bravo AF: 0.657

Asia WGS AF: 0.756 AC: 2630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.58
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12677663; hg19: chr8-74007347;