rs8177235

chr3-133757239-G-A

Variant summary

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

The NM_001063.4(TF):c.870+230G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0757 in 152,232 control chromosomes in the GnomAD database, including 562 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 0.076 (562 hom., cov: 32)
• Consequence: TF NM_001063.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

Genes affected

TF (HGNC:11740): (transferrin) This gene encodes a glycoprotein with an approximate molecular weight of 76.5 kDa. It is thought to have been created as a result of an ancient gene duplication event that led to generation of homologous C and N-terminal domains each of which binds one ion of ferric iron. The function of this protein is to transport iron from the intestine, reticuloendothelial system, and liver parenchymal cells to all proliferating cells in the body. This protein may also have a physiologic role as granulocyte/pollen-binding protein (GPBP) involved in the removal of certain organic matter and allergens from serum. [provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TF	NM_001063.4	c.870+230G>A		intron_variant		ENST00000402696.9
TF	NM_001354703.2	c.738+230G>A		intron_variant
TF	NM_001354704.2	c.489+230G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TF	ENST00000402696.9	c.870+230G>A		intron_variant		1	NM_001063.4	P1
TF	ENST00000485977.1	c.235+230G>A		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0757 AC: 11519 AN: 152114 Hom.: 559 Cov.: 32

Gnomad AFR AF: 0.0640

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0590

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0796

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0615

Gnomad OTH AF: 0.0817

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

GnomAD4 genome AF: 0.0757 AC: 11527 AN: 152232 Hom.: 562 Cov.: 32 AF XY: 0.0790 AC XY: 5883 AN XY: 74432

Gnomad4 AFR AF: 0.0642

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0590

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0796

Gnomad4 NFE AF: 0.0615

Gnomad4 OTH AF: 0.0823

Alfa AF: 0.0706 Hom.: 121

Bravo AF: 0.0784

Asia WGS AF: 0.178 AC: 618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	3.9
Dann	Benign	0.75

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: rs8177235; hg19: chr3-133476083;