chr7-11642149-C-T

Variant names:

• chr7-11642149-C-T
• rs6460831
• NM_015204.3:c.191-5188G>A

Variant summary

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

The NM_015204.3(THSD7A):​c.191-5188G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 151,942 control chromosomes in the GnomAD database, including 11,153 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 0.38 (11153 hom., cov: 32)
• Consequence: THSD7A NM_015204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THSD7A	NM_015204.3	c.191-5188G>A		intron_variant	Intron 1 of 27	ENST00000423059.9	NP_056019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THSD7A	ENST00000423059.9	c.191-5188G>A		intron_variant	Intron 1 of 27	5	NM_015204.3	ENSP00000406482.2
THSD7A	ENST00000480061.1	n.218-5188G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57696 AN: 151824 Hom.: 11150 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.380 AC: 57719 AN: 151942 Hom.: 11153 Cov.: 32 AF XY: 0.387 AC XY: 28732 AN XY: 74248

African (AFR) AF: 0.397 AC: 16454 AN: 41444

American (AMR) AF: 0.317 AC: 4835 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1368 AN: 3462

East Asian (EAS) AF: 0.502 AC: 2594 AN: 5170

South Asian (SAS) AF: 0.598 AC: 2884 AN: 4822

European-Finnish (FIN) AF: 0.412 AC: 4345 AN: 10552

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.354 AC: 24022 AN: 67942

Other (OTH) AF: 0.372 AC: 784 AN: 2110

Alfa AF: 0.362 Hom.: 18019

Bravo AF: 0.367

Asia WGS AF: 0.564 AC: 1963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.8
DANN	Benign	0.41
PhyloP100		-0.17
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: rs6460831; hg19: chr7-11681776;