chr7-11563272-T-C

Variant summary

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

The NM_015204.3(THSD7A):​c.1454-20155A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 152,064 control chromosomes in the GnomAD database, including 24,280 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 0.56 ( 24280 hom., cov: 32)

Consequence

THSD7A
NM_015204.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.22

Publications

17 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]

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=-0.79).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
THSD7ANM_015204.3 linkc.1454-20155A>G intron_variant Intron 4 of 27 ENST00000423059.9 NP_056019.1 Q9UPZ6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
THSD7AENST00000423059.9 linkc.1454-20155A>G intron_variant Intron 4 of 27 5 NM_015204.3 ENSP00000406482.2 Q9UPZ6

Frequencies

GnomAD3 genomes
AF:
0.562
AC:
85319
AN:
151946
Hom.:
24254
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.525
Gnomad AMI
AF:
0.378
Gnomad AMR
AF:
0.661
Gnomad ASJ
AF:
0.648
Gnomad EAS
AF:
0.528
Gnomad SAS
AF:
0.566
Gnomad FIN
AF:
0.498
Gnomad MID
AF:
0.674
Gnomad NFE
AF:
0.570
Gnomad OTH
AF:
0.596
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.561
AC:
85382
AN:
152064
Hom.:
24280
Cov.:
32
AF XY:
0.560
AC XY:
41624
AN XY:
74320
show subpopulations
African (AFR)
AF:
0.525
AC:
21774
AN:
41490
American (AMR)
AF:
0.661
AC:
10098
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
0.648
AC:
2249
AN:
3470
East Asian (EAS)
AF:
0.528
AC:
2722
AN:
5154
South Asian (SAS)
AF:
0.564
AC:
2727
AN:
4832
European-Finnish (FIN)
AF:
0.498
AC:
5260
AN:
10556
Middle Eastern (MID)
AF:
0.670
AC:
197
AN:
294
European-Non Finnish (NFE)
AF:
0.570
AC:
38755
AN:
67968
Other (OTH)
AF:
0.594
AC:
1255
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1918
3836
5753
7671
9589
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
720
1440
2160
2880
3600
<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:
0.574
Hom.:
78341
Bravo
AF:
0.573
Asia WGS
AF:
0.543
AC:
1887
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
0.52
DANN
Benign
0.63
PhyloP100
-1.2
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

Other links and lift over

dbSNP: rs16; hg19: chr7-11602899; API