rs10950366

chr7-11751995-A-C

Variant summary

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

The NM_015204.3(THSD7A):c.190+79762T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,074 control chromosomes in the GnomAD database, including 5,480 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 0.22 (5480 hom., cov: 32)
• Consequence: THSD7A NM_015204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
THSD7A	NM_015204.3	c.190+79762T>G		intron_variant		ENST00000423059.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THSD7A	ENST00000423059.9	c.190+79762T>G		intron_variant		5	NM_015204.3	P1

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33862 AN: 151956 Hom.: 5457 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0737

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.223 AC: 33936 AN: 152074 Hom.: 5480 Cov.: 32 AF XY: 0.228 AC XY: 16937 AN XY: 74326

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.0737

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.185

Alfa AF: 0.146 Hom.: 858

Bravo AF: 0.223

Asia WGS AF: 0.251 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.8
Dann	Benign	0.23

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: rs10950366; hg19: chr7-11791621;