Menu
GeneBe

7-11375812-A-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_015204.3(THSD7A):c.4956T>C(p.Asp1652=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00525 in 1,612,644 control chromosomes in the GnomAD database, including 251 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.023 ( 130 hom., cov: 32)
Exomes 𝑓: 0.0034 ( 121 hom. )

Consequence

THSD7A
NM_015204.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.88
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 made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-11375812-A-G is Benign according to our data. Variant chr7-11375812-A-G is described in ClinVar as [Benign]. Clinvar id is 775247.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=1.88 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0708 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
THSD7ANM_015204.3 linkuse as main transcriptc.4956T>C p.Asp1652= synonymous_variant 28/28 ENST00000423059.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
THSD7AENST00000423059.9 linkuse as main transcriptc.4956T>C p.Asp1652= synonymous_variant 28/285 NM_015204.3 P1
ENST00000445839.5 linkuse as main transcriptn.247-3475A>G intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0225
AC:
3414
AN:
152062
Hom.:
127
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0730
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0156
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.0000942
Gnomad MID
AF:
0.0538
Gnomad NFE
AF:
0.00132
Gnomad OTH
AF:
0.0201
GnomAD3 exomes
AF:
0.00703
AC:
1748
AN:
248708
Hom.:
60
AF XY:
0.00576
AC XY:
777
AN XY:
134924
show subpopulations
Gnomad AFR exome
AF:
0.0767
Gnomad AMR exome
AF:
0.00839
Gnomad ASJ exome
AF:
0.000797
Gnomad EAS exome
AF:
0.000390
Gnomad SAS exome
AF:
0.000295
Gnomad FIN exome
AF:
0.000139
Gnomad NFE exome
AF:
0.00187
Gnomad OTH exome
AF:
0.00614
GnomAD4 exome
AF:
0.00345
AC:
5033
AN:
1460464
Hom.:
121
Cov.:
30
AF XY:
0.00315
AC XY:
2289
AN XY:
726514
show subpopulations
Gnomad4 AFR exome
AF:
0.0797
Gnomad4 AMR exome
AF:
0.00897
Gnomad4 ASJ exome
AF:
0.000690
Gnomad4 EAS exome
AF:
0.000202
Gnomad4 SAS exome
AF:
0.000278
Gnomad4 FIN exome
AF:
0.0000749
Gnomad4 NFE exome
AF:
0.00121
Gnomad4 OTH exome
AF:
0.00796
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0225
AC:
3431
AN:
152180
Hom.:
130
Cov.:
32
AF XY:
0.0219
AC XY:
1633
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.0730
Gnomad4 AMR
AF:
0.0157
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.0000942
Gnomad4 NFE
AF:
0.00132
Gnomad4 OTH
AF:
0.0232
Alfa
AF:
0.0118
Hom.:
23
Bravo
AF:
0.0261
Asia WGS
AF:
0.0180
AC:
62
AN:
3478
EpiCase
AF:
0.00164
EpiControl
AF:
0.00220

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 submitterclinical testingInvitaeJun 27, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.51
Cadd
Benign
6.3
Dann
Benign
0.71

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs56264449; hg19: chr7-11415439; API