rs10280061

chr7-11566419-T-C

Variant summary

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

The NM_015204.3(THSD7A):c.1454-23302A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,034 control chromosomes in the GnomAD database, including 20,437 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 0.52 (20437 hom., cov: 32)
• Consequence: THSD7A NM_015204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

Genes affected

THSD7A (HGNC:22207): (thrombospondin type 1 domain containing 7A) The protein encoded by this gene is found almost exclusively in endothelial cells from placenta and umbilical cord. The encoded protein appears to interact with alpha(V)beta(3) integrin and paxillin to inhibit endothelial cell migration and tube formation. This protein may be involved in cytoskeletal organization. Variations in this gene may be associated with low bone mineral density in osteoporosis. [provided by RefSeq, Aug 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
THSD7A	NM_015204.3	c.1454-23302A>G		intron_variant		ENST00000423059.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THSD7A	ENST00000423059.9	c.1454-23302A>G		intron_variant		5	NM_015204.3	P1

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78454 AN: 151914 Hom.: 20412 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.516 AC: 78523 AN: 152034 Hom.: 20437 Cov.: 32 AF XY: 0.516 AC XY: 38317 AN XY: 74324

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.513

Alfa AF: 0.512 Hom.: 9944

Bravo AF: 0.516

Asia WGS AF: 0.555 AC: 1933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.4
Dann	Benign	0.35

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: rs10280061; hg19: chr7-11606046;