3-133761614-T-A

Position:

• chr3-133761614-T-A

Variant summary

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

The NM_001063.4(TF):​c.1203+2285T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 152,252 control chromosomes in the GnomAD database, including 8,618 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 0.33 (8608 hom., cov: 33)
  • Exomes 𝑓: 0.49 (10 hom.)
• Consequence: TF NM_001063.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.23

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TF	NM_001063.4	c.1203+2285T>A		intron_variant		ENST00000402696.9	NP_001054.2
TF	NM_001354703.2	c.1071+2285T>A		intron_variant			NP_001341632.2
TF	NM_001354704.2	c.822+2285T>A		intron_variant			NP_001341633.2
ACSL3P1		n.133761614T>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TF	ENST00000402696.9	c.1203+2285T>A		intron_variant		1	NM_001063.4	ENSP00000385834.3
ACSL3P1	ENST00000474389.1	n.1168T>A		non_coding_transcript_exon_variant	2/2	6

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50235 AN: 152042 Hom.: 8588 Cov.: 33

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.333

GnomAD4 exome AF: 0.489 AC: 45 AN: 92 Hom.: 10 Cov.: 0 AF XY: 0.462 AC XY: 24 AN XY: 52

Gnomad4 FIN exome AF: 0.515

Gnomad4 NFE exome AF: 0.409

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.331 AC: 50298 AN: 152160 Hom.: 8608 Cov.: 33 AF XY: 0.331 AC XY: 24623 AN XY: 74372

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.339

Alfa AF: 0.339 Hom.: 1220

Bravo AF: 0.336

Asia WGS AF: 0.426 AC: 1479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.0
DANN	Benign	0.84

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: rs8177260; hg19: chr3-133480458;