dbSNP rs2074597: THSD7A:c.191-106G>T (chr7-11637067-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015204.3(THSD7A):c.191-106G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 1,045,734 control chromosomes in the GnomAD database, including 29,847 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 0.29 ( 7542 hom., cov: 32)

Exomes 𝑓: 0.21 ( 22305 hom. )

Consequence

THSD7A
NM_015204.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.475

Publications

8 publications found

Variant links:

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]

THSD7A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THSD7A	NM_015204.3 link	c.191-106G>T		intron_variant	Intron 1 of 27	ENST00000423059.9	NP_056019.1	Q9UPZ6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THSD7A	ENST00000423059.9 link	c.191-106G>T		intron_variant	Intron 1 of 27	5	NM_015204.3	ENSP00000406482.2		Q9UPZ6
THSD7A	ENST00000480061.1 link	n.218-106G>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.289

AC:

43880

AN:

151914

Hom.:

7527

Cov.:

show subpopulations

Gnomad AFR

AF:

0.472

Gnomad AMI

AF:

0.195

Gnomad AMR

AF:

0.264

Gnomad ASJ

AF:

0.258

Gnomad EAS

AF:

0.461

Gnomad SAS

AF:

0.215

Gnomad FIN

AF:

0.216

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.190

Gnomad OTH

AF:

0.282

GnomAD4 exome

AF:

0.208

AC:

185548

AN:

893702

Hom.:

22305

AF XY:

0.207

AC XY:

93230

AN XY:

450496

show subpopulations

African (AFR)

AF:

0.481

AC:

10081

AN:

20940

American (AMR)

AF:

0.251

AC:

5887

AN:

23418

Ashkenazi Jewish (ASJ)

AF:

0.251

AC:

4226

AN:

16866

East Asian (EAS)

AF:

0.484

AC:

17078

AN:

35280

South Asian (SAS)

AF:

0.212

AC:

12096

AN:

57174

European-Finnish (FIN)

AF:

0.209

AC:

6897

AN:

33032

Middle Eastern (MID)

AF:

0.263

AC:

1151

AN:

4376

European-Non Finnish (NFE)

AF:

0.179

AC:

118601

AN:

661684

Other (OTH)

AF:

0.233

AC:

9531

AN:

40932

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

7481

14962

22444

29925

37406

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3638

7276

10914

14552

18190

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.289

AC:

43942

AN:

152032

Hom.:

7542

Cov.:

AF XY:

0.289

AC XY:

21501

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.472

AC:

19564

AN:

41434

American (AMR)

AF:

0.263

AC:

4026

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.258

AC:

896

AN:

3472

East Asian (EAS)

AF:

0.460

AC:

2371

AN:

5150

South Asian (SAS)

AF:

0.216

AC:

1044

AN:

4824

European-Finnish (FIN)

AF:

0.216

AC:

2279

AN:

10568

Middle Eastern (MID)

AF:

0.255

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.190

AC:

12919

AN:

67978

Other (OTH)

AF:

0.279

AC:

590

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1495

2990

4484

5979

7474

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

434

868

1302

1736

2170

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.216

Hom.:

7466

Bravo

AF:

0.304

Asia WGS

AF:

0.330

AC:

1148

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

(source)

DANN

Benign

0.67

PhyloP100

0.47

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over