7-11565705-T-C

Variant names:

• chr7-11565705-T-C
• rs82
• NM_015204.3:c.1454-22588A>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.1454-22588A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,132 control chromosomes in the GnomAD database, including 52,456 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 0.83 (52456 hom., cov: 32)
• Consequence: THSD7A NM_015204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 0 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THSD7A	NM_015204.3	c.1454-22588A>G		intron_variant	Intron 4 of 27	ENST00000423059.9	NP_056019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THSD7A	ENST00000423059.9	c.1454-22588A>G		intron_variant	Intron 4 of 27	5	NM_015204.3	ENSP00000406482.2

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125663 AN: 152012 Hom.: 52405 Cov.: 32

Gnomad AFR AF: 0.922

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.895

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.827 AC: 125769 AN: 152132 Hom.: 52456 Cov.: 32 AF XY: 0.828 AC XY: 61616 AN XY: 74384

African (AFR) AF: 0.922 AC: 38274 AN: 41514

American (AMR) AF: 0.887 AC: 13556 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3023 AN: 3470

East Asian (EAS) AF: 0.765 AC: 3948 AN: 5164

South Asian (SAS) AF: 0.763 AC: 3680 AN: 4824

European-Finnish (FIN) AF: 0.789 AC: 8340 AN: 10576

Middle Eastern (MID) AF: 0.887 AC: 259 AN: 292

European-Non Finnish (NFE) AF: 0.772 AC: 52455 AN: 67984

Other (OTH) AF: 0.821 AC: 1735 AN: 2114

Alfa AF: 0.783 Hom.: 21771

Bravo AF: 0.839

Asia WGS AF: 0.776 AC: 2700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.36
PhyloP100		-0.64
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: rs82; hg19: chr7-11605332;