rs1526538

Variant names:

• chr7-11734614-G-A
• rs1526538
• NM_015204.3:c.190+97143C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-11734614-G-A
• chr7-11734614-G-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.190+97143C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,720 control chromosomes in the GnomAD database, including 20,158 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 0.49 (20158 hom., cov: 32)
• Consequence: THSD7A NM_015204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THSD7A	NM_015204.3	c.190+97143C>T		intron_variant	Intron 1 of 27	ENST00000423059.9	NP_056019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THSD7A	ENST00000423059.9	c.190+97143C>T		intron_variant	Intron 1 of 27	5	NM_015204.3	ENSP00000406482.2
THSD7A	ENST00000480061.1	n.217+16523C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74828 AN: 151600 Hom.: 20169 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.493 AC: 74828 AN: 151720 Hom.: 20158 Cov.: 32 AF XY: 0.493 AC XY: 36541 AN XY: 74088

African (AFR) AF: 0.257 AC: 10657 AN: 41414

American (AMR) AF: 0.575 AC: 8731 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2253 AN: 3466

East Asian (EAS) AF: 0.423 AC: 2160 AN: 5108

South Asian (SAS) AF: 0.512 AC: 2467 AN: 4818

European-Finnish (FIN) AF: 0.575 AC: 6066 AN: 10550

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40793 AN: 67866

Other (OTH) AF: 0.508 AC: 1072 AN: 2112

Alfa AF: 0.562 Hom.: 25821

Bravo AF: 0.484

Asia WGS AF: 0.468 AC: 1619 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.70
PhyloP100		0.22
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: rs1526538; hg19: chr7-11774241;