chr7-11554610-G-A

Variant names:

• chr7-11554610-G-A
• rs31
• NM_015204.3:c.1454-11493C>T

Variant summary

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

The NM_015204.3(THSD7A):​c.1454-11493C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 151,890 control chromosomes in the GnomAD database, including 51,705 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 0.82 (51705 hom., cov: 31)
• Consequence: THSD7A NM_015204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THSD7A	NM_015204.3	c.1454-11493C>T		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.1454-11493C>T		intron_variant	Intron 4 of 27	5	NM_015204.3	ENSP00000406482.2

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124587 AN: 151772 Hom.: 51649 Cov.: 31

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.821 AC: 124698 AN: 151890 Hom.: 51705 Cov.: 31 AF XY: 0.820 AC XY: 60901 AN XY: 74244

African (AFR) AF: 0.926 AC: 38416 AN: 41496

American (AMR) AF: 0.887 AC: 13496 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3014 AN: 3468

East Asian (EAS) AF: 0.752 AC: 3884 AN: 5164

South Asian (SAS) AF: 0.740 AC: 3552 AN: 4800

European-Finnish (FIN) AF: 0.732 AC: 7725 AN: 10550

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52127 AN: 67894

Other (OTH) AF: 0.821 AC: 1728 AN: 2106

Alfa AF: 0.790 Hom.: 9591

Bravo AF: 0.838

Asia WGS AF: 0.754 AC: 2623 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.29
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

Publications

LitVar

Other links and lift over

dbSNP: rs31; hg19: chr7-11594237;