chr2-70489467-T-C

Variant names:

• chr2-70489467-T-C
• rs2902345
• NM_003236.4:c.95-23731A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003236.4(TGFA):​c.95-23731A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 152,138 control chromosomes in the GnomAD database, including 25,297 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 0.57 (25297 hom., cov: 33)
• Consequence: TGFA NM_003236.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 12 publications found

Genes affected

TGFA (HGNC:11765): (transforming growth factor alpha) This gene encodes a growth factor that is a ligand for the epidermal growth factor receptor, which activates a signaling pathway for cell proliferation, differentiation and development. This protein may act as either a transmembrane-bound ligand or a soluble ligand. This gene has been associated with many types of cancers, and it may also be involved in some cases of cleft lip/palate. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

TGFA Gene-Disease associations (from GenCC):

• tooth agenesis

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003236.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TGFA	NM_003236.4	MANE Select	c.95-23731A>G		intron	N/A	NP_003227.1	P01135-1
	TGFA	NM_001308158.2		c.113-23731A>G		intron	N/A	NP_001295087.1	F8VNR3
	TGFA	NM_001308159.2		c.113-23734A>G		intron	N/A	NP_001295088.1	E7EPT6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TGFA	ENST00000295400.11	TSL:1 MANE Select	c.95-23731A>G		intron	N/A	ENSP00000295400.6	P01135-1
	TGFA	ENST00000444975.5	TSL:1	c.113-23731A>G		intron	N/A	ENSP00000404131.1	F8VNR3
	TGFA	ENST00000450929.5	TSL:1	c.113-23734A>G		intron	N/A	ENSP00000414127.1	E7EPT6

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86972 AN: 152020 Hom.: 25270 Cov.: 33

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.572 AC: 87048 AN: 152138 Hom.: 25297 Cov.: 33 AF XY: 0.573 AC XY: 42598 AN XY: 74354

African (AFR) AF: 0.654 AC: 27149 AN: 41528

American (AMR) AF: 0.593 AC: 9061 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1321 AN: 3472

East Asian (EAS) AF: 0.609 AC: 3138 AN: 5156

South Asian (SAS) AF: 0.512 AC: 2467 AN: 4818

European-Finnish (FIN) AF: 0.580 AC: 6135 AN: 10582

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35912 AN: 67980

Other (OTH) AF: 0.563 AC: 1189 AN: 2112

Alfa AF: 0.572 Hom.: 3525

Bravo AF: 0.581

Asia WGS AF: 0.564 AC: 1963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.70
DANN	Benign	0.29
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2902345; hg19: chr2-70716599;