1-218346056-GCACACACACACACACA-GCACACACACACA

Variant names:

• chr1-218346056-GCACA-G
• rs151329324
• NM_003238.6:c.-624_-621delACAC

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The NM_003238.6(TGFB2):​c.-624_-621delACAC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0102 in 145,656 control chromosomes in the GnomAD database, including 10 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.010 (10 hom., cov: 28)
• Consequence: TGFB2 NM_003238.6 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.0102 (1489/145656) while in subpopulation EAS AF = 0.036 (170/4720). AF 95% confidence interval is 0.0316. There are 10 homozygotes in GnomAd4. There are 737 alleles in the male GnomAd4 subpopulation. Median coverage is 28. This position passed quality control check.
• BS2: High AC in GnomAd4 at 1489 AD,Unknown gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003238.6. 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
	TGFB2	NM_003238.6	MANE Select	c.-624_-621delACAC		5_prime_UTR	Exon 1 of 7	NP_003229.1	P61812-1
	TGFB2	NM_001135599.4		c.-624_-621delACAC		5_prime_UTR	Exon 1 of 8	NP_001129071.1	P61812-2
	TGFB2	NR_138148.2		n.743_746delACAC		non_coding_transcript_exon	Exon 1 of 7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TGFB2	ENST00000366930.9	TSL:1 MANE Select	c.-624_-621delACAC		5_prime_UTR	Exon 1 of 7	ENSP00000355897.4	P61812-1
	TGFB2-AS1	ENST00000774588.1		n.239-672_239-669delTGTG		intron	N/A
	TGFB2-AS1	ENST00000774589.1		n.32-672_32-669delTGTG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0102 AC: 1492 AN: 145578 Hom.: 10 Cov.: 28

Gnomad AFR AF: 0.00886

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00456

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.0363

Gnomad SAS AF: 0.0162

Gnomad FIN AF: 0.0137

Gnomad MID AF: 0.0390

Gnomad NFE AF: 0.00929

Gnomad OTH AF: 0.0131

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

GnomAD4 genome AF: 0.0102 AC: 1489 AN: 145656 Hom.: 10 Cov.: 28 AF XY: 0.0104 AC XY: 737 AN XY: 70944

African (AFR) AF: 0.00884 AC: 351 AN: 39696

American (AMR) AF: 0.00456 AC: 67 AN: 14702

Ashkenazi Jewish (ASJ) AF: 0.0141 AC: 48 AN: 3398

East Asian (EAS) AF: 0.0360 AC: 170 AN: 4720

South Asian (SAS) AF: 0.0162 AC: 71 AN: 4392

European-Finnish (FIN) AF: 0.0137 AC: 132 AN: 9644

Middle Eastern (MID) AF: 0.0390 AC: 11 AN: 282

European-Non Finnish (NFE) AF: 0.00929 AC: 613 AN: 65950

Other (OTH) AF: 0.0130 AC: 26 AN: 1996

Alfa AF: 0.00269 Hom.: 1

Bravo AF: 0.00969

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs151329324; hg19: chr1-218519398;