chr7-11563272-T-C

Variant names:

• chr7-11563272-T-C
• rs16
• NM_015204.3:c.1454-20155A>G

Variant summary

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

The NM_015204.3(THSD7A):​c.1454-20155A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 152,064 control chromosomes in the GnomAD database, including 24,280 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 0.56 (24280 hom., cov: 32)
• Consequence: THSD7A NM_015204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 17 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=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THSD7A	NM_015204.3	c.1454-20155A>G		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.1454-20155A>G		intron_variant	Intron 4 of 27	5	NM_015204.3	ENSP00000406482.2

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85319 AN: 151946 Hom.: 24254 Cov.: 32

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.561 AC: 85382 AN: 152064 Hom.: 24280 Cov.: 32 AF XY: 0.560 AC XY: 41624 AN XY: 74320

African (AFR) AF: 0.525 AC: 21774 AN: 41490

American (AMR) AF: 0.661 AC: 10098 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2249 AN: 3470

East Asian (EAS) AF: 0.528 AC: 2722 AN: 5154

South Asian (SAS) AF: 0.564 AC: 2727 AN: 4832

European-Finnish (FIN) AF: 0.498 AC: 5260 AN: 10556

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38755 AN: 67968

Other (OTH) AF: 0.594 AC: 1255 AN: 2114

Alfa AF: 0.574 Hom.: 78341

Bravo AF: 0.573

Asia WGS AF: 0.543 AC: 1887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.52
DANN	Benign	0.63
PhyloP100		-1.2
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: rs16; hg19: chr7-11602899;