rs2284792

Positions:

• chr14-75977236-G-A
• chr14-75977236-G-C
• chr14-75977236-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003239.5(TGFB3):​c.352+3306C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,136 control chromosomes in the GnomAD database, including 33,691 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 0.65 (33691 hom., cov: 33)
• Consequence: TGFB3 NM_003239.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

Genes affected

TGFB3 (HGNC:11769): (transforming growth factor beta 3) 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. This protein is involved in embryogenesis and cell differentiation, and may play a role in wound healing. Mutations in this gene are a cause of aortic aneurysms and dissections, as well as familial arrhythmogenic right ventricular dysplasia 1. [provided by RefSeq, Aug 2016]

IFT43 (HGNC:29669): (intraflagellar transport 43) This gene encodes a subunit of the intraflagellar transport complex A (IFT-A). IFT-A is a multiprotein complex that plays an important role in cilia assembly and maintenance by mediating retrograde ciliary transport. Mutations in this gene are a cause of cranioectodermal dysplasia-3 (CED3), also known as Sensenbrenner syndrome. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TGFB3	NM_003239.5	c.352+3306C>T		intron_variant		ENST00000238682.8	NP_003230.1
TGFB3	NM_001329938.2	c.352+3306C>T		intron_variant			NP_001316867.1
TGFB3	NM_001329939.2	c.352+3306C>T		intron_variant			NP_001316868.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TGFB3	ENST00000238682.8	c.352+3306C>T		intron_variant		1	NM_003239.5	ENSP00000238682	P1
TGFB3	ENST00000556285.1	c.352+3306C>T		intron_variant		1		ENSP00000451110
TGFB3	ENST00000556674.2	c.352+3306C>T		intron_variant		3		ENSP00000502685	P1
IFT43	ENST00000555677.5	n.90-11649G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98846 AN: 152018 Hom.: 33686 Cov.: 33

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.650 AC: 98867 AN: 152136 Hom.: 33691 Cov.: 33 AF XY: 0.654 AC XY: 48611 AN XY: 74382

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.726

Gnomad4 EAS AF: 0.582

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.832

Gnomad4 NFE AF: 0.742

Gnomad4 OTH AF: 0.635

Alfa AF: 0.706 Hom.: 19051

Bravo AF: 0.632

Asia WGS AF: 0.611 AC: 2125 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	0.041
DANN	Benign	0.73

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

Other links and lift over

dbSNP: rs2284792; hg19: chr14-76443579;