rs37

chr7-11550587-C-T

Variant summary

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

The NM_015204.3(THSD7A):c.1454-7470G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,118 control chromosomes in the GnomAD database, including 4,045 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 0.20 (4045 hom., cov: 32)
• Consequence: THSD7A NM_015204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290

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=-0.48).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
THSD7A	NM_015204.3	c.1454-7470G>A		intron_variant		ENST00000423059.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THSD7A	ENST00000423059.9	c.1454-7470G>A		intron_variant		5	NM_015204.3	P1

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30832 AN: 152000 Hom.: 4041 Cov.: 32

Gnomad AFR AF: 0.0548

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.203 AC: 30829 AN: 152118 Hom.: 4045 Cov.: 32 AF XY: 0.204 AC XY: 15178 AN XY: 74362

Gnomad4 AFR AF: 0.0546

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.245

Alfa AF: 0.221 Hom.: 508

Bravo AF: 0.212

Asia WGS AF: 0.170 AC: 591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
Cadd	Benign	12
Dann	Benign	0.94

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: rs37; hg19: chr7-11590214;