chr15-39584380-C-T
Position:
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_003246.4(THBS1):c.984C>T(p.Asn328=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00052 in 1,614,144 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00063 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00051 ( 4 hom. )
Consequence
THBS1
NM_003246.4 synonymous
NM_003246.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.77
Genes affected
THBS1 (HGNC:11785): (thrombospondin 1) The protein encoded by this gene is a subunit of a disulfide-linked homotrimeric protein. This protein is an adhesive glycoprotein that mediates cell-to-cell and cell-to-matrix interactions. This protein can bind to fibrinogen, fibronectin, laminin, type V collagen and integrins alpha-V/beta-1. This protein has been shown to play roles in platelet aggregation, angiogenesis, and tumorigenesis. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 15-39584380-C-T is Benign according to our data. Variant chr15-39584380-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 774713.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-3.77 with no splicing effect.
BS2
High AC in GnomAd4 at 96 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THBS1 | NM_003246.4 | c.984C>T | p.Asn328= | synonymous_variant | 6/22 | ENST00000260356.6 | |
THBS1 | XM_047432980.1 | c.984C>T | p.Asn328= | synonymous_variant | 6/22 | ||
THBS1 | XM_011521971.3 | c.984C>T | p.Asn328= | synonymous_variant | 6/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THBS1 | ENST00000260356.6 | c.984C>T | p.Asn328= | synonymous_variant | 6/22 | 1 | NM_003246.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000631 AC: 96AN: 152136Hom.: 0 Cov.: 33
GnomAD3 genomes
AF:
AC:
96
AN:
152136
Hom.:
Cov.:
33
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:
GnomAD3 exomes AF: 0.000958 AC: 241AN: 251482Hom.: 1 AF XY: 0.000942 AC XY: 128AN XY: 135914
GnomAD3 exomes
AF:
AC:
241
AN:
251482
Hom.:
AF XY:
AC XY:
128
AN XY:
135914
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000509 AC: 744AN: 1461890Hom.: 4 Cov.: 32 AF XY: 0.000498 AC XY: 362AN XY: 727246
GnomAD4 exome
AF:
AC:
744
AN:
1461890
Hom.:
Cov.:
32
AF XY:
AC XY:
362
AN XY:
727246
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.000631 AC: 96AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.000484 AC XY: 36AN XY: 74452
GnomAD4 genome
AF:
AC:
96
AN:
152254
Hom.:
Cov.:
33
AF XY:
AC XY:
36
AN XY:
74452
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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