rs8177252

Variant names:

• chr3-133761330-C-A
• rs8177252
• NM_001063.4:c.1203+2001C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-133761330-C-A
• chr3-133761330-C-G
• chr3-133761330-C-T

Variant summary

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

The NM_001063.4(TF):​c.1203+2001C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 158,634 control chromosomes in the GnomAD database, including 8,333 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 0.32 (7901 hom., cov: 31)
  • Exomes 𝑓: 0.35 (432 hom.)
• Consequence: TF NM_001063.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.19
• Publications: 3 publications found

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]

ACSL3P1 (HGNC:56529): (ACSL3 pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001063.4. 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
	TF	NM_001063.4	MANE Select	c.1203+2001C>A		intron	N/A	NP_001054.2	P02787
	TF	NM_001354703.2		c.1071+2001C>A		intron	N/A	NP_001341632.2
	TF	NM_001354704.2		c.822+2001C>A		intron	N/A	NP_001341633.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TF	ENST00000402696.9	TSL:1 MANE Select	c.1203+2001C>A		intron	N/A	ENSP00000385834.3	P02787
	TF	ENST00000877249.1		c.555+2001C>A		intron	N/A	ENSP00000547308.1
	TF	ENST00000877246.1		c.217-2852C>A		intron	N/A	ENSP00000547305.1

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47914 AN: 151654 Hom.: 7889 Cov.: 31

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.318

GnomAD4 exome AF: 0.345 AC: 2370 AN: 6862 Hom.: 432 Cov.: 0 AF XY: 0.340 AC XY: 1452 AN XY: 4274

African (AFR) AF: 0.209 AC: 36 AN: 172

American (AMR) AF: 0.509 AC: 357 AN: 702

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 37 AN: 144

East Asian (EAS) AF: 0.414 AC: 163 AN: 394

South Asian (SAS) AF: 0.425 AC: 291 AN: 684

European-Finnish (FIN) AF: 0.308 AC: 267 AN: 866

Middle Eastern (MID) AF: 0.286 AC: 4 AN: 14

European-Non Finnish (NFE) AF: 0.311 AC: 1109 AN: 3568

Other (OTH) AF: 0.333 AC: 106 AN: 318

GnomAD4 genome AF: 0.316 AC: 47968 AN: 151772 Hom.: 7901 Cov.: 31 AF XY: 0.318 AC XY: 23545 AN XY: 74140

African (AFR) AF: 0.242 AC: 10031 AN: 41424

American (AMR) AF: 0.387 AC: 5895 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 988 AN: 3464

East Asian (EAS) AF: 0.425 AC: 2190 AN: 5150

South Asian (SAS) AF: 0.424 AC: 2032 AN: 4796

European-Finnish (FIN) AF: 0.286 AC: 3001 AN: 10508

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22804 AN: 67884

Other (OTH) AF: 0.320 AC: 673 AN: 2104

Alfa AF: 0.240 Hom.: 1116

Bravo AF: 0.320

Asia WGS AF: 0.402 AC: 1399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	1.2
DANN	Benign	0.56
PhyloP100		2.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs8177252; hg19: chr3-133480174;