rs11165354

Variant summary

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

The NM_003243.5(TGFBR3):​c.738-959G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 151,940 control chromosomes in the GnomAD database, including 24,529 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 0.55 ( 24529 hom., cov: 31)

Consequence

TGFBR3
NM_003243.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.212
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=-0.86).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TGFBR3NM_003243.5 linkuse as main transcriptc.738-959G>T intron_variant ENST00000212355.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TGFBR3ENST00000212355.9 linkuse as main transcriptc.738-959G>T intron_variant 1 NM_003243.5 P3Q03167-1

Frequencies

GnomAD3 genomes
AF:
0.548
AC:
83213
AN:
151820
Hom.:
24515
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.322
Gnomad AMI
AF:
0.552
Gnomad AMR
AF:
0.645
Gnomad ASJ
AF:
0.786
Gnomad EAS
AF:
0.505
Gnomad SAS
AF:
0.799
Gnomad FIN
AF:
0.532
Gnomad MID
AF:
0.666
Gnomad NFE
AF:
0.638
Gnomad OTH
AF:
0.578
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.548
AC:
83259
AN:
151940
Hom.:
24529
Cov.:
31
AF XY:
0.548
AC XY:
40716
AN XY:
74252
show subpopulations
Gnomad4 AFR
AF:
0.323
Gnomad4 AMR
AF:
0.645
Gnomad4 ASJ
AF:
0.786
Gnomad4 EAS
AF:
0.506
Gnomad4 SAS
AF:
0.799
Gnomad4 FIN
AF:
0.532
Gnomad4 NFE
AF:
0.638
Gnomad4 OTH
AF:
0.577
Alfa
AF:
0.627
Hom.:
39525
Bravo
AF:
0.540
Asia WGS
AF:
0.633
AC:
2203
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
5.4
DANN
Benign
0.70

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: rs11165354; hg19: chr1-92194322; API