rs12332694

chr5-80046166-C-A

Variant summary

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

The NM_003248.6(THBS4):c.292+5886C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,072 control chromosomes in the GnomAD database, including 6,132 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 (6132 hom., cov: 32)
• Consequence: THBS4 NM_003248.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

Genes affected

THBS4 (HGNC:11788): (thrombospondin 4) The protein encoded by this gene belongs to the thrombospondin protein family. Thrombospondin family members are adhesive glycoproteins that mediate cell-to-cell and cell-to-matrix interactions. This protein forms a pentamer and can bind to heparin and calcium. It is involved in local signaling in the developing and adult nervous system, and it contributes to spinal sensitization and neuropathic pain states. This gene is activated during the stromal response to invasive breast cancer. It may also play a role in inflammatory responses in Alzheimer's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]

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 (NFE) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
THBS4	NM_003248.6	c.292+5886C>A		intron_variant		ENST00000350881.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THBS4	ENST00000350881.6	c.292+5886C>A		intron_variant		1	NM_003248.6	P1
THBS4	ENST00000511733.1	c.19+5886C>A		intron_variant		2
THBS4	ENST00000510218.1	n.381+5886C>A		intron_variant, non_coding_transcript_variant		4
THBS4	ENST00000513310.5	n.350+5886C>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41481 AN: 151954 Hom.: 6125 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.273 AC: 41511 AN: 152072 Hom.: 6132 Cov.: 32 AF XY: 0.270 AC XY: 20046 AN XY: 74336

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.282

Alfa AF: 0.283 Hom.: 1271

Bravo AF: 0.268

Asia WGS AF: 0.260 AC: 907 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	5.9
Dann	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs12332694; hg19: chr5-79341989; COSMIC: COSV63467972;