rs10262606

chr7-11520332-G-Achr7-11520332-G-T

Variant summary

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

The NM_015204.3(THSD7A):c.1822+21087C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,020 control chromosomes in the GnomAD database, including 2,352 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 0.16 (2352 hom., cov: 32)
• Consequence: THSD7A NM_015204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261

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 (AFR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
THSD7A	NM_015204.3	c.1822+21087C>T		intron_variant		ENST00000423059.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THSD7A	ENST00000423059.9	c.1822+21087C>T		intron_variant		5	NM_015204.3	P1
THSD7A	ENST00000497575.1	n.311+21087C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24554 AN: 151900 Hom.: 2351 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0661

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.162 AC: 24584 AN: 152020 Hom.: 2352 Cov.: 32 AF XY: 0.164 AC XY: 12212 AN XY: 74282

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.0661

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.137

Alfa AF: 0.0716 Hom.: 75

Bravo AF: 0.166

Asia WGS AF: 0.116 AC: 404 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	5.0
Dann	Benign	0.70

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: rs10262606; hg19: chr7-11559959;