rs6972615

Positions:

• chr7-11514469-A-G

Variant summary

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

The NM_015204.3(THSD7A):​c.1822+26950T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,070 control chromosomes in the GnomAD database, including 3,568 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 0.21 (3568 hom., cov: 32)
• Consequence: THSD7A NM_015204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
THSD7A	NM_015204.3	c.1822+26950T>C		intron_variant		ENST00000423059.9	NP_056019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
THSD7A	ENST00000423059.9	c.1822+26950T>C		intron_variant		5	NM_015204.3	ENSP00000406482	P1
	ENST00000445839.5	n.442-5583A>G		intron_variant, non_coding_transcript_variant		4
THSD7A	ENST00000497575.1	n.311+26950T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32542 AN: 151954 Hom.: 3562 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.214 AC: 32560 AN: 152070 Hom.: 3568 Cov.: 32 AF XY: 0.212 AC XY: 15762 AN XY: 74316

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.226

Alfa AF: 0.225 Hom.: 5276

Bravo AF: 0.214

Asia WGS AF: 0.195 AC: 679 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.64
DANN	Benign	0.40

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: rs6972615; hg19: chr7-11554096;