NM_015204.3:c.1822+11312T>C

Variant names:

• chr7-11530107-A-G
• rs6963353
• NM_015204.3:c.1822+11312T>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.1822+11312T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 152,048 control chromosomes in the GnomAD database, including 29,557 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 0.62 (29557 hom., cov: 32)
• Consequence: THSD7A NM_015204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THSD7A	NM_015204.3	MANE Select	c.1822+11312T>C		intron	N/A	NP_056019.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THSD7A	ENST00000423059.9	TSL:5 MANE Select	c.1822+11312T>C		intron	N/A	ENSP00000406482.2
	THSD7A	ENST00000497575.1	TSL:5	n.311+11312T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94040 AN: 151930 Hom.: 29544 Cov.: 32

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.619 AC: 94084 AN: 152048 Hom.: 29557 Cov.: 32 AF XY: 0.618 AC XY: 45912 AN XY: 74310

African (AFR) AF: 0.548 AC: 22719 AN: 41450

American (AMR) AF: 0.505 AC: 7720 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2151 AN: 3466

East Asian (EAS) AF: 0.777 AC: 4013 AN: 5166

South Asian (SAS) AF: 0.758 AC: 3660 AN: 4830

European-Finnish (FIN) AF: 0.604 AC: 6380 AN: 10566

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.665 AC: 45183 AN: 67982

Other (OTH) AF: 0.613 AC: 1293 AN: 2110

Alfa AF: 0.641 Hom.: 53467

Bravo AF: 0.603

Asia WGS AF: 0.714 AC: 2482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.41
PhyloP100		-0.23
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: rs6963353; hg19: chr7-11569734;