rs1467345

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015204.3(THSD7A):​c.190+87467C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 151,574 control chromosomes in the GnomAD database, including 5,111 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 0.22 ( 5111 hom., cov: 32)

Consequence

THSD7A
NM_015204.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0980
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
THSD7ANM_015204.3 linkuse as main transcriptc.190+87467C>T intron_variant ENST00000423059.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
THSD7AENST00000423059.9 linkuse as main transcriptc.190+87467C>T intron_variant 5 NM_015204.3 P1
THSD7AENST00000480061.1 linkuse as main transcriptn.217+6847C>T intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.217
AC:
32838
AN:
151454
Hom.:
5092
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.440
Gnomad AMI
AF:
0.180
Gnomad AMR
AF:
0.135
Gnomad ASJ
AF:
0.0750
Gnomad EAS
AF:
0.163
Gnomad SAS
AF:
0.274
Gnomad FIN
AF:
0.201
Gnomad MID
AF:
0.142
Gnomad NFE
AF:
0.111
Gnomad OTH
AF:
0.174
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.217
AC:
32903
AN:
151574
Hom.:
5111
Cov.:
32
AF XY:
0.222
AC XY:
16409
AN XY:
74014
show subpopulations
Gnomad4 AFR
AF:
0.439
Gnomad4 AMR
AF:
0.135
Gnomad4 ASJ
AF:
0.0750
Gnomad4 EAS
AF:
0.163
Gnomad4 SAS
AF:
0.276
Gnomad4 FIN
AF:
0.201
Gnomad4 NFE
AF:
0.111
Gnomad4 OTH
AF:
0.179
Alfa
AF:
0.145
Hom.:
1520
Bravo
AF:
0.216
Asia WGS
AF:
0.234
AC:
816
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.79
DANN
Benign
0.38

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: rs1467345; hg19: chr7-11783917; API