rs45

chr7-11546515-A-Cchr7-11546515-A-Gchr7-11546515-A-T

Variant summary

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

The NM_015204.3(THSD7A):c.1454-3398T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 152,058 control chromosomes in the GnomAD database, including 46,076 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 0.77 (46076 hom., cov: 32)
• Consequence: THSD7A NM_015204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
THSD7A	NM_015204.3	c.1454-3398T>G		intron_variant		ENST00000423059.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THSD7A	ENST00000423059.9	c.1454-3398T>G		intron_variant		5	NM_015204.3	P1

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117315 AN: 151940 Hom.: 46029 Cov.: 32

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.772 AC: 117418 AN: 152058 Hom.: 46076 Cov.: 32 AF XY: 0.771 AC XY: 57260 AN XY: 74304

Gnomad4 AFR AF: 0.904

Gnomad4 AMR AF: 0.843

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.777

Alfa AF: 0.741 Hom.: 5262

Bravo AF: 0.792

Asia WGS AF: 0.697 AC: 2427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.40
Dann	Benign	0.64

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: rs45; hg19: chr7-11586142;