rs10486135

chr7-11488873-C-A

Variant summary

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

The NM_015204.3(THSD7A):c.1823-6891G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 151,858 control chromosomes in the GnomAD database, including 12,478 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 0.40 (12478 hom., cov: 32)
• Consequence: THSD7A NM_015204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

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]

(HGNC:):

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 = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
THSD7A	NM_015204.3	c.1823-6891G>T		intron_variant		ENST00000423059.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THSD7A	ENST00000423059.9	c.1823-6891G>T		intron_variant		5	NM_015204.3	P1
	ENST00000445839.5	n.442-31179C>A		intron_variant, non_coding_transcript_variant		4
THSD7A	ENST00000497575.1	n.312-41449G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61033 AN: 151740 Hom.: 12459 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.402 AC: 61108 AN: 151858 Hom.: 12478 Cov.: 32 AF XY: 0.398 AC XY: 29515 AN XY: 74228

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.411

Alfa AF: 0.413 Hom.: 27166

Bravo AF: 0.405

Asia WGS AF: 0.411 AC: 1425 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	1.9
Dann	Benign	0.75

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: rs10486135; hg19: chr7-11528500;