7-11816611-C-G

Variant summary

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

The NM_015204.3(THSD7A):c.190+15146G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,782 control chromosomes in the GnomAD database, including 8,092 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 0.32 (8092 hom., cov: 33)
• Consequence: THSD7A NM_015204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
THSD7A	NM_015204.3	c.190+15146G>C		intron_variant		ENST00000423059.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THSD7A	ENST00000423059.9	c.190+15146G>C		intron_variant		5	NM_015204.3	P1

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48482 AN: 151660 Hom.: 8083 Cov.: 33

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.320 AC: 48532 AN: 151782 Hom.: 8092 Cov.: 33 AF XY: 0.320 AC XY: 23722 AN XY: 74194

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.331

Alfa AF: 0.176 Hom.: 343

Bravo AF: 0.341

Asia WGS AF: 0.381 AC: 1324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.40
Dann	Benign	0.35

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: rs10270630; hg19: chr7-11856237;