rs2107479

Positions:

• chr7-11560413-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.1454-17296A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,070 control chromosomes in the GnomAD database, including 4,594 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 0.23 (4594 hom., cov: 32)
• Consequence: THSD7A NM_015204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
THSD7A	NM_015204.3	c.1454-17296A>G		intron_variant		ENST00000423059.9	NP_056019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
THSD7A	ENST00000423059.9	c.1454-17296A>G		intron_variant		5	NM_015204.3	ENSP00000406482	P1

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35156 AN: 151956 Hom.: 4587 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.231 AC: 35179 AN: 152070 Hom.: 4594 Cov.: 32 AF XY: 0.232 AC XY: 17208 AN XY: 74318

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.261

Alfa AF: 0.260 Hom.: 7317

Bravo AF: 0.243

Asia WGS AF: 0.180 AC: 626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.73
DANN	Benign	0.85

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: rs2107479; hg19: chr7-11600040;