rs1007750

Positions:

• chr8-73074057-A-C
• chr8-73074057-A-G
• chr8-73074057-A-T

Variant summary

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

The NM_153225.4(SBSPON):​c.410-2187T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 152,042 control chromosomes in the GnomAD database, including 12,464 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 0.39 (12464 hom., cov: 32)
• Consequence: SBSPON NM_153225.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SBSPON	NM_153225.4	c.410-2187T>G		intron_variant		ENST00000297354.7	NP_694957.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SBSPON	ENST00000297354.7	c.410-2187T>G		intron_variant		1	NM_153225.4	ENSP00000297354	P1
SBSPON	ENST00000519697.1	n.778-2187T>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59147 AN: 151924 Hom.: 12465 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.389 AC: 59181 AN: 152042 Hom.: 12464 Cov.: 32 AF XY: 0.398 AC XY: 29608 AN XY: 74318

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.817

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.414

Alfa AF: 0.365 Hom.: 10920

Bravo AF: 0.402

Asia WGS AF: 0.634 AC: 2205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.34
DANN	Benign	0.60

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: rs1007750; hg19: chr8-73986292;