rs1800277

Positions:

• chr3-133747311-C-T

Variant summary

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

The NM_001063.4(TF):​c.43+828C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0692 in 152,420 control chromosomes in the GnomAD database, including 445 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 0.069 (445 hom., cov: 33)
  • Exomes 𝑓: 0.079 (0 hom.)
• Consequence: TF NM_001063.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

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]

TF (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TF	NM_001063.4	c.43+828C>T		intron_variant		ENST00000402696.9	NP_001054.2
TF	NM_001354703.2	c.-89-1101C>T		intron_variant			NP_001341632.2
TF	NM_001354704.2	c.-166+828C>T		intron_variant			NP_001341633.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TF	ENST00000402696.9	c.43+828C>T		intron_variant		1	NM_001063.4	ENSP00000385834.3

Frequencies

GnomAD3 genomes AF: 0.0690 AC: 10504 AN: 152188 Hom.: 440 Cov.: 33

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0443

Gnomad ASJ AF: 0.0778

Gnomad EAS AF: 0.0531

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0835

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0485

Gnomad OTH AF: 0.0583

GnomAD4 exome AF: 0.0789 AC: 9 AN: 114 Hom.: 0 Cov.: 0 AF XY: 0.0667 AC XY: 6 AN XY: 90

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.0900

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0692 AC: 10538 AN: 152306 Hom.: 445 Cov.: 33 AF XY: 0.0708 AC XY: 5277 AN XY: 74484

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.0442

Gnomad4 ASJ AF: 0.0778

Gnomad4 EAS AF: 0.0530

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0835

Gnomad4 NFE AF: 0.0485

Gnomad4 OTH AF: 0.0591

Alfa AF: 0.0714 Hom.: 91

Bravo AF: 0.0675

Asia WGS AF: 0.0830 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.6
DANN	Benign	0.43

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: rs1800277; hg19: chr3-133466155;