rs1467345

Variant names:

• chr7-11744290-G-A
• rs1467345
• NM_015204.3:c.190+87467C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-11744290-G-A
• chr7-11744290-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.96).
• 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 rank	MANE	Protein	UniProt
THSD7A	NM_015204.3	c.190+87467C>T		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.190+87467C>T		intron_variant	Intron 1 of 27	5	NM_015204.3	ENSP00000406482.2
THSD7A	ENST00000480061.1	n.217+6847C>T		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.439 AC: 18181 AN: 41368

American (AMR) AF: 0.135 AC: 2046 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.0750 AC: 260 AN: 3466

East Asian (EAS) AF: 0.163 AC: 829 AN: 5098

South Asian (SAS) AF: 0.276 AC: 1328 AN: 4820

European-Finnish (FIN) AF: 0.201 AC: 2121 AN: 10544

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7555 AN: 67794

Other (OTH) AF: 0.179 AC: 378 AN: 2108

Alfa AF: 0.147 Hom.: 1879

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
PhyloP100		-0.098
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: rs1467345; hg19: chr7-11783917;