rs17575497

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_003243.5(TGFBR3):​c.61+11132G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0104 in 152,244 control chromosomes in the GnomAD database, including 19 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 0.010 ( 19 hom., cov: 31)

Consequence

TGFBR3
NM_003243.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.28
Variant links:
Genes affected
TGFBR3 (HGNC:11774): (transforming growth factor beta receptor 3) This locus encodes the transforming growth factor (TGF)-beta type III receptor. The encoded receptor is a membrane proteoglycan that often functions as a co-receptor with other TGF-beta receptor superfamily members. Ectodomain shedding produces soluble TGFBR3, which may inhibit TGFB signaling. Decreased expression of this receptor has been observed in various cancers. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene.[provided by RefSeq, Sep 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BS2
High AC in GnomAd4 at 1581 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TGFBR3NM_003243.5 linkuse as main transcriptc.61+11132G>A intron_variant ENST00000212355.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TGFBR3ENST00000212355.9 linkuse as main transcriptc.61+11132G>A intron_variant 1 NM_003243.5 P3Q03167-1

Frequencies

GnomAD3 genomes
AF:
0.0104
AC:
1581
AN:
152126
Hom.:
19
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00220
Gnomad AMI
AF:
0.00879
Gnomad AMR
AF:
0.0103
Gnomad ASJ
AF:
0.00260
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.0361
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0135
Gnomad OTH
AF:
0.00621
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0104
AC:
1581
AN:
152244
Hom.:
19
Cov.:
31
AF XY:
0.0110
AC XY:
820
AN XY:
74434
show subpopulations
Gnomad4 AFR
AF:
0.00219
Gnomad4 AMR
AF:
0.0103
Gnomad4 ASJ
AF:
0.00260
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.0361
Gnomad4 NFE
AF:
0.0135
Gnomad4 OTH
AF:
0.00615
Alfa
AF:
0.0100
Hom.:
4
Bravo
AF:
0.00847
Asia WGS
AF:
0.000577
AC:
2
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
3.5
DANN
Benign
0.60

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: rs17575497; hg19: chr1-92315896; API