7-11638151-T-C

Variant names:

• chr7-11638151-T-C
• rs2526100
• NM_015204.3:c.191-1190A>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.191-1190A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,138 control chromosomes in the GnomAD database, including 1,810 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 0.15 (1810 hom., cov: 32)
• Consequence: THSD7A NM_015204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015204.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THSD7A	NM_015204.3	MANE Select	c.191-1190A>G		intron	N/A	NP_056019.1	Q9UPZ6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THSD7A	ENST00000423059.9	TSL:5 MANE Select	c.191-1190A>G		intron	N/A	ENSP00000406482.2	Q9UPZ6
	THSD7A	ENST00000480061.1	TSL:3	n.218-1190A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22636 AN: 152020 Hom.: 1805 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.0692

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.0616

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.149 AC: 22658 AN: 152138 Hom.: 1810 Cov.: 32 AF XY: 0.149 AC XY: 11066 AN XY: 74366

African (AFR) AF: 0.120 AC: 4969 AN: 41512

American (AMR) AF: 0.206 AC: 3154 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0692 AC: 240 AN: 3470

East Asian (EAS) AF: 0.173 AC: 894 AN: 5168

South Asian (SAS) AF: 0.0610 AC: 294 AN: 4816

European-Finnish (FIN) AF: 0.154 AC: 1634 AN: 10592

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11006 AN: 67986

Other (OTH) AF: 0.147 AC: 310 AN: 2106

Alfa AF: 0.156 Hom.: 354

Bravo AF: 0.154

Asia WGS AF: 0.124 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.80
PhyloP100		-0.73
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: rs2526100; hg19: chr7-11677778;