1-91683720-C-T

Variant summary

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

The NM_003243.5(TGFBR3):​c.*19G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 1,406,694 control chromosomes in the GnomAD database, including 19,366 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 0.14 ( 1601 hom., cov: 32)
Exomes 𝑓: 0.17 ( 17765 hom. )

Consequence

TGFBR3
NM_003243.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.122
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=-0.49).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TGFBR3NM_003243.5 linkc.*19G>A 3_prime_UTR_variant Exon 17 of 17 ENST00000212355.9 NP_003234.2 Q03167-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TGFBR3ENST00000212355 linkc.*19G>A 3_prime_UTR_variant Exon 17 of 17 1 NM_003243.5 ENSP00000212355.4 Q03167-1

Frequencies

GnomAD3 genomes
AF:
0.143
AC:
20695
AN:
145188
Hom.:
1597
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0907
Gnomad AMI
AF:
0.219
Gnomad AMR
AF:
0.127
Gnomad ASJ
AF:
0.138
Gnomad EAS
AF:
0.130
Gnomad SAS
AF:
0.122
Gnomad FIN
AF:
0.173
Gnomad MID
AF:
0.163
Gnomad NFE
AF:
0.175
Gnomad OTH
AF:
0.128
GnomAD3 exomes
AF:
0.135
AC:
20295
AN:
150396
Hom.:
1496
AF XY:
0.136
AC XY:
10892
AN XY:
80192
show subpopulations
Gnomad AFR exome
AF:
0.0807
Gnomad AMR exome
AF:
0.0920
Gnomad ASJ exome
AF:
0.145
Gnomad EAS exome
AF:
0.117
Gnomad SAS exome
AF:
0.106
Gnomad FIN exome
AF:
0.153
Gnomad NFE exome
AF:
0.171
Gnomad OTH exome
AF:
0.135
GnomAD4 exome
AF:
0.173
AC:
218654
AN:
1261374
Hom.:
17765
Cov.:
31
AF XY:
0.173
AC XY:
107550
AN XY:
621954
show subpopulations
Gnomad4 AFR exome
AF:
0.0960
Gnomad4 AMR exome
AF:
0.107
Gnomad4 ASJ exome
AF:
0.179
Gnomad4 EAS exome
AF:
0.161
Gnomad4 SAS exome
AF:
0.110
Gnomad4 FIN exome
AF:
0.226
Gnomad4 NFE exome
AF:
0.181
Gnomad4 OTH exome
AF:
0.170
GnomAD4 genome
AF:
0.143
AC:
20713
AN:
145320
Hom.:
1601
Cov.:
32
AF XY:
0.142
AC XY:
10077
AN XY:
70826
show subpopulations
Gnomad4 AFR
AF:
0.0912
Gnomad4 AMR
AF:
0.127
Gnomad4 ASJ
AF:
0.138
Gnomad4 EAS
AF:
0.130
Gnomad4 SAS
AF:
0.122
Gnomad4 FIN
AF:
0.173
Gnomad4 NFE
AF:
0.175
Gnomad4 OTH
AF:
0.127
Alfa
AF:
0.106
Hom.:
216
Bravo
AF:
0.134

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.49
CADD
Benign
5.3
DANN
Benign
0.88
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: rs1131243; hg19: chr1-92149277; API