rs1467345

Positions:

• chr7-11744290-G-A
• chr7-11744290-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.190+87467C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 151,574 control chromosomes in the GnomAD database, including 5,111 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 (5111 hom., cov: 32)
• Consequence: THSD7A NM_015204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

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 = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
THSD7A	NM_015204.3	c.190+87467C>T		intron_variant		ENST00000423059.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THSD7A	ENST00000423059.9	c.190+87467C>T		intron_variant		5	NM_015204.3	P1
THSD7A	ENST00000480061.1	n.217+6847C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32838 AN: 151454 Hom.: 5092 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0750

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.217 AC: 32903 AN: 151574 Hom.: 5111 Cov.: 32 AF XY: 0.222 AC XY: 16409 AN XY: 74014

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.0750

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.179

Alfa AF: 0.145 Hom.: 1520

Bravo AF: 0.216

Asia WGS AF: 0.234 AC: 816 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.79
DANN	Benign	0.38

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: rs1467345; hg19: chr7-11783917;