chr7-11556875-A-G

Variant names:

• chr7-11556875-A-G
• rs22
• NM_015204.3:c.1454-13758T>C

Variant summary

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

The NM_015204.3(THSD7A):​c.1454-13758T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 151,692 control chromosomes in the GnomAD database, including 28,332 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 0.61 (28332 hom., cov: 31)
• Consequence: THSD7A NM_015204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 0 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THSD7A	NM_015204.3	c.1454-13758T>C		intron_variant	Intron 4 of 27	ENST00000423059.9	NP_056019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THSD7A	ENST00000423059.9	c.1454-13758T>C		intron_variant	Intron 4 of 27	5	NM_015204.3	ENSP00000406482.2

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91712 AN: 151574 Hom.: 28296 Cov.: 31

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.676

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.605 AC: 91799 AN: 151692 Hom.: 28332 Cov.: 31 AF XY: 0.602 AC XY: 44650 AN XY: 74136

African (AFR) AF: 0.724 AC: 29967 AN: 41414

American (AMR) AF: 0.658 AC: 10011 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2100 AN: 3470

East Asian (EAS) AF: 0.560 AC: 2875 AN: 5134

South Asian (SAS) AF: 0.533 AC: 2563 AN: 4808

European-Finnish (FIN) AF: 0.510 AC: 5363 AN: 10508

Middle Eastern (MID) AF: 0.669 AC: 194 AN: 290

European-Non Finnish (NFE) AF: 0.547 AC: 37113 AN: 67826

Other (OTH) AF: 0.612 AC: 1292 AN: 2110

Alfa AF: 0.581 Hom.: 7633

Bravo AF: 0.622

Asia WGS AF: 0.534 AC: 1852 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.29
PhyloP100		-1.5
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: rs22; hg19: chr7-11596502; COSMIC: COSV70274355;