1-218346025-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_003238.6(TGFB2):c.-677T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 150,444 control chromosomes in the GnomAD database, including 13,242 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.39 (13242 hom., cov: 28)
• Consequence: TGFB2 NM_003238.6 5_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.257

Genes affected

TGFB2 (HGNC:11768): (transforming growth factor beta 2) This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate a latency-associated peptide (LAP) and a mature peptide, and is found in either a latent form composed of a mature peptide homodimer, a LAP homodimer, and a latent TGF-beta binding protein, or in an active form consisting solely of the mature peptide homodimer. The mature peptide may also form heterodimers with other TGF-beta family members. Disruption of the TGF-beta/SMAD pathway has been implicated in a variety of human cancers. A chromosomal translocation that includes this gene is associated with Peters' anomaly, a congenital defect of the anterior chamber of the eye. Mutations in this gene may be associated with Loeys-Dietz syndrome. This gene encodes multiple isoforms that may undergo similar proteolytic processing. [provided by RefSeq, Aug 2016]

TGFB2-AS1 (HGNC:50628): (TGFB2 antisense RNA 1 (head to head))

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BP6: Variant 1-218346025-T-C is Benign according to our data. Variant chr1-218346025-T-C is described in ClinVar as [Benign]. Clinvar id is 295468.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TGFB2	NM_003238.6	c.-677T>C		5_prime_UTR_variant	1/7	ENST00000366930.9
TGFB2	NM_001135599.4	c.-677T>C		5_prime_UTR_variant	1/8
TGFB2	NR_138148.2	n.690T>C		non_coding_transcript_exon_variant	1/7
TGFB2	NR_138149.2	n.690T>C		non_coding_transcript_exon_variant	1/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TGFB2	ENST00000366930.9	c.-677T>C		5_prime_UTR_variant	1/7	1	NM_003238.6	P1
TGFB2-AS1	ENST00000689961.2	n.12A>G		non_coding_transcript_exon_variant	1/3
TGFB2-AS1	ENST00000414452.2			upstream_gene_variant		3
TGFB2-AS1	ENST00000691401.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.385 AC: 57841 AN: 150336 Hom.: 13210 Cov.: 28

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.337

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.348

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.385 AC: 57932 AN: 150444 Hom.: 13242 Cov.: 28 AF XY: 0.383 AC XY: 28142 AN XY: 73460

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.351

Alfa AF: 0.329 Hom.: 1197

Bravo AF: 0.399

Asia WGS AF: 0.364 AC: 1263 AN: 3474

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Loeys-Dietz syndrome 4 Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Apr 27, 2017

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 26, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
Cadd	Benign	20
Dann	Benign	0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs112369231; hg19: chr1-218519367;