rs1043237

chr11-14267507-A-T

Variant summary

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

The NM_006108.4(SPON1):c.*1820A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,020 control chromosomes in the GnomAD database, including 6,265 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 0.27 (6265 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SPON1 NM_006108.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

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]

SPON1-AS1 (HGNC:53117): (SPON1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPON1	NM_006108.4	c.*1820A>T		3_prime_UTR_variant	16/16	ENST00000576479.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPON1	ENST00000576479.4	c.*1820A>T		3_prime_UTR_variant	16/16	1	NM_006108.4	P1
SPON1-AS1	ENST00000534587.1	n.39-4460T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40877 AN: 151902 Hom.: 6263 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.267

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.269 AC: 40895 AN: 152020 Hom.: 6265 Cov.: 32 AF XY: 0.275 AC XY: 20455 AN XY: 74266

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.269

Alfa AF: 0.297 Hom.: 922

Bravo AF: 0.252

Asia WGS AF: 0.335 AC: 1166 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.44
Dann	Benign	0.66

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: rs1043237; hg19: chr11-14289053;