chr7-11563272-T-C
Variant names:
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
NM_015204.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.22
Publications
17 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]
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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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.562 AC: 85319AN: 151946Hom.: 24254 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
85319
AN:
151946
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.561 AC: 85382AN: 152064Hom.: 24280 Cov.: 32 AF XY: 0.560 AC XY: 41624AN XY: 74320 show subpopulations
GnomAD4 genome
AF:
AC:
85382
AN:
152064
Hom.:
Cov.:
32
AF XY:
AC XY:
41624
AN XY:
74320
show subpopulations
African (AFR)
AF:
AC:
21774
AN:
41490
American (AMR)
AF:
AC:
10098
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
AC:
2249
AN:
3470
East Asian (EAS)
AF:
AC:
2722
AN:
5154
South Asian (SAS)
AF:
AC:
2727
AN:
4832
European-Finnish (FIN)
AF:
AC:
5260
AN:
10556
Middle Eastern (MID)
AF:
AC:
197
AN:
294
European-Non Finnish (NFE)
AF:
AC:
38755
AN:
67968
Other (OTH)
AF:
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
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1887
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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