rs902

Variant summary

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

The NM_003243.5(TGFBR3):​c.*1069G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 453,748 control chromosomes in the GnomAD database, including 137,443 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 0.79 ( 47878 hom., cov: 29)
Exomes 𝑓: 0.77 ( 89565 hom. )

Consequence

TGFBR3
NM_003243.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.513
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TGFBR3NM_003243.5 linkuse as main transcriptc.*1069G>C 3_prime_UTR_variant 17/17 ENST00000212355.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TGFBR3ENST00000212355.9 linkuse as main transcriptc.*1069G>C 3_prime_UTR_variant 17/171 NM_003243.5 P3Q03167-1

Frequencies

GnomAD3 genomes
AF:
0.790
AC:
119988
AN:
151834
Hom.:
47811
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.868
Gnomad AMI
AF:
0.704
Gnomad AMR
AF:
0.770
Gnomad ASJ
AF:
0.732
Gnomad EAS
AF:
0.985
Gnomad SAS
AF:
0.815
Gnomad FIN
AF:
0.793
Gnomad MID
AF:
0.755
Gnomad NFE
AF:
0.735
Gnomad OTH
AF:
0.777
GnomAD3 exomes
AF:
0.785
AC:
102470
AN:
130460
Hom.:
40689
AF XY:
0.784
AC XY:
55847
AN XY:
71214
show subpopulations
Gnomad AFR exome
AF:
0.875
Gnomad AMR exome
AF:
0.772
Gnomad ASJ exome
AF:
0.741
Gnomad EAS exome
AF:
0.991
Gnomad SAS exome
AF:
0.803
Gnomad FIN exome
AF:
0.790
Gnomad NFE exome
AF:
0.739
Gnomad OTH exome
AF:
0.754
GnomAD4 exome
AF:
0.767
AC:
231592
AN:
301796
Hom.:
89565
Cov.:
0
AF XY:
0.770
AC XY:
132420
AN XY:
171996
show subpopulations
Gnomad4 AFR exome
AF:
0.868
Gnomad4 AMR exome
AF:
0.771
Gnomad4 ASJ exome
AF:
0.743
Gnomad4 EAS exome
AF:
0.991
Gnomad4 SAS exome
AF:
0.803
Gnomad4 FIN exome
AF:
0.778
Gnomad4 NFE exome
AF:
0.736
Gnomad4 OTH exome
AF:
0.765
GnomAD4 genome
AF:
0.790
AC:
120112
AN:
151952
Hom.:
47878
Cov.:
29
AF XY:
0.794
AC XY:
58996
AN XY:
74256
show subpopulations
Gnomad4 AFR
AF:
0.868
Gnomad4 AMR
AF:
0.770
Gnomad4 ASJ
AF:
0.732
Gnomad4 EAS
AF:
0.985
Gnomad4 SAS
AF:
0.815
Gnomad4 FIN
AF:
0.793
Gnomad4 NFE
AF:
0.736
Gnomad4 OTH
AF:
0.779
Alfa
AF:
0.756
Hom.:
7730
Bravo
AF:
0.792
Asia WGS
AF:
0.891
AC:
3102
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.1
DANN
Benign
0.50
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs902; hg19: chr1-92148227; API