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GeneBe

7-11379660-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2

The NM_015204.3(THSD7A):c.4560G>A(p.Pro1520=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00172 in 1,592,152 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0076 ( 13 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 17 hom. )

Consequence

THSD7A
NM_015204.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.57
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 -13 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=-0.37).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-11379660-C-T is Benign according to our data. Variant chr7-11379660-C-T is described in ClinVar as [Benign]. Clinvar id is 776208.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=-1.57 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00758 (1155/152278) while in subpopulation AFR AF= 0.0254 (1057/41562). AF 95% confidence interval is 0.0242. There are 13 homozygotes in gnomad4. There are 550 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 13 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
THSD7ANM_015204.3 linkuse as main transcriptc.4560G>A p.Pro1520= synonymous_variant 25/28 ENST00000423059.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
THSD7AENST00000423059.9 linkuse as main transcriptc.4560G>A p.Pro1520= synonymous_variant 25/285 NM_015204.3 P1
ENST00000445839.5 linkuse as main transcriptn.329+291C>T intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00758
AC:
1153
AN:
152160
Hom.:
13
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0255
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00314
Gnomad ASJ
AF:
0.00835
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000176
Gnomad OTH
AF:
0.00383
GnomAD3 exomes
AF:
0.00196
AC:
427
AN:
217632
Hom.:
4
AF XY:
0.00149
AC XY:
174
AN XY:
116752
show subpopulations
Gnomad AFR exome
AF:
0.0224
Gnomad AMR exome
AF:
0.00131
Gnomad ASJ exome
AF:
0.00579
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000189
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000312
Gnomad OTH exome
AF:
0.00147
GnomAD4 exome
AF:
0.00110
AC:
1577
AN:
1439874
Hom.:
17
Cov.:
31
AF XY:
0.000986
AC XY:
704
AN XY:
713778
show subpopulations
Gnomad4 AFR exome
AF:
0.0264
Gnomad4 AMR exome
AF:
0.00141
Gnomad4 ASJ exome
AF:
0.00698
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000242
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000220
Gnomad4 OTH exome
AF:
0.00299
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00758
AC:
1155
AN:
152278
Hom.:
13
Cov.:
33
AF XY:
0.00739
AC XY:
550
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.0254
Gnomad4 AMR
AF:
0.00314
Gnomad4 ASJ
AF:
0.00835
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000176
Gnomad4 OTH
AF:
0.00379
Alfa
AF:
0.00408
Hom.:
3
Bravo
AF:
0.00824
Asia WGS
AF:
0.00260
AC:
9
AN:
3478

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 testingInvitaeFeb 20, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.37
Cadd
Benign
11
Dann
Benign
0.84

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.080
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: rs17164530; hg19: chr7-11419287; API