7-11530107-A-G

Position:

• chr7-11530107-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
THSD7A	NM_015204.3	c.1822+11312T>C		intron_variant		ENST00000423059.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THSD7A	ENST00000423059.9	c.1822+11312T>C		intron_variant		5	NM_015204.3	P1
THSD7A	ENST00000497575.1	n.311+11312T>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.758

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.613

Alfa AF: 0.647 Hom.: 42942

Bravo AF: 0.603

Asia WGS AF: 0.714 AC: 2482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.41

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

Publications

LitVar

Other links and lift over

dbSNP: rs6963353; hg19: chr7-11569734;