rs10280061

Variant names:

• chr7-11566419-T-C
• rs10280061
• NM_015204.3:c.1454-23302A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015204.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THSD7A	NM_015204.3	MANE Select	c.1454-23302A>G		intron	N/A	NP_056019.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THSD7A	ENST00000423059.9	TSL:5 MANE Select	c.1454-23302A>G		intron	N/A	ENSP00000406482.2

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

African (AFR) AF: 0.565 AC: 23439 AN: 41496

American (AMR) AF: 0.451 AC: 6898 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1891 AN: 3470

East Asian (EAS) AF: 0.538 AC: 2765 AN: 5144

South Asian (SAS) AF: 0.604 AC: 2911 AN: 4818

European-Finnish (FIN) AF: 0.432 AC: 4558 AN: 10544

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34442 AN: 67968

Other (OTH) AF: 0.513 AC: 1082 AN: 2110

Alfa AF: 0.510 Hom.: 13785

Bravo AF: 0.516

Asia WGS AF: 0.555 AC: 1933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.35
PhyloP100		-0.16
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10280061; hg19: chr7-11606046;