7-11478143-T-C

Variant names:

• chr7-11478143-T-C
• rs7793532
• NM_015204.3:c.2018-3575A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015204.3(THSD7A):​c.2018-3575A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 152,026 control chromosomes in the GnomAD database, including 43,694 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 0.76 (43694 hom., cov: 31)
• Consequence: THSD7A NM_015204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 3 publications found

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]

ENSG00000230333 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THSD7A	NM_015204.3	c.2018-3575A>G		intron_variant	Intron 7 of 27	ENST00000423059.9	NP_056019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THSD7A	ENST00000423059.9	c.2018-3575A>G		intron_variant	Intron 7 of 27	5	NM_015204.3	ENSP00000406482.2
ENSG00000230333	ENST00000445839.5	n.442-41909T>C		intron_variant	Intron 3 of 3	4
THSD7A	ENST00000497575.1	n.312-30719A>G		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115187 AN: 151908 Hom.: 43648 Cov.: 31

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.755

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.758 AC: 115291 AN: 152026 Hom.: 43694 Cov.: 31 AF XY: 0.762 AC XY: 56636 AN XY: 74302

African (AFR) AF: 0.750 AC: 31092 AN: 41456

American (AMR) AF: 0.789 AC: 12066 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2638 AN: 3470

East Asian (EAS) AF: 0.718 AC: 3702 AN: 5158

South Asian (SAS) AF: 0.829 AC: 3993 AN: 4818

European-Finnish (FIN) AF: 0.793 AC: 8372 AN: 10556

Middle Eastern (MID) AF: 0.757 AC: 221 AN: 292

European-Non Finnish (NFE) AF: 0.749 AC: 50904 AN: 67968

Other (OTH) AF: 0.760 AC: 1606 AN: 2114

Alfa AF: 0.750 Hom.: 11613

Bravo AF: 0.756

Asia WGS AF: 0.800 AC: 2782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.68
PhyloP100		0.011
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7793532; hg19: chr7-11517770;