7-11406947-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_015204.3(THSD7A):c.4025G>A(p.Arg1342Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000998 in 1,613,794 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0047 ( 5 hom., cov: 32)
Exomes 𝑓: 0.00061 ( 4 hom. )
Consequence
THSD7A
NM_015204.3 missense
NM_015204.3 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: 0.162
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 made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0054184496).
BP6
?
Variant 7-11406947-C-T is Benign according to our data. Variant chr7-11406947-C-T is described in ClinVar as [Benign]. Clinvar id is 781897.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 5 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THSD7A | NM_015204.3 | c.4025G>A | p.Arg1342Gln | missense_variant | 21/28 | ENST00000423059.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THSD7A | ENST00000423059.9 | c.4025G>A | p.Arg1342Gln | missense_variant | 21/28 | 5 | NM_015204.3 | P1 | |
ENST00000445839.5 | n.441+23039C>T | intron_variant, non_coding_transcript_variant | 4 | ||||||
ENST00000425837.1 | upstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00474 AC: 721AN: 152114Hom.: 5 Cov.: 32
GnomAD3 genomes
?
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152114
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GnomAD3 exomes AF: 0.00142 AC: 353AN: 248726Hom.: 3 AF XY: 0.00106 AC XY: 143AN XY: 134942
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GnomAD4 exome AF: 0.000608 AC: 889AN: 1461562Hom.: 4 Cov.: 31 AF XY: 0.000576 AC XY: 419AN XY: 727054
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GnomAD4 genome ? AF: 0.00474 AC: 722AN: 152232Hom.: 5 Cov.: 32 AF XY: 0.00450 AC XY: 335AN XY: 74442
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195
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 04, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N;.
REVEL
Benign
Sift
Benign
T;.
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at