3-133760782-C-T

Position:

• chr3-133760782-C-T

Variant summary

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

The ENST00000402696.9(TF):​c.1203+1453C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 162,034 control chromosomes in the GnomAD database, including 7,160 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 0.28 (6994 hom., cov: 33)
  • Exomes 𝑓: 0.17 (166 hom.)
• Consequence: TF ENST00000402696.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290

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=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TF	NM_001063.4	c.1203+1453C>T		intron_variant		ENST00000402696.9	NP_001054.2
TF	NM_001354703.2	c.1071+1453C>T		intron_variant			NP_001341632.2
TF	NM_001354704.2	c.822+1453C>T		intron_variant			NP_001341633.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TF	ENST00000402696.9	c.1203+1453C>T		intron_variant		1	NM_001063.4	ENSP00000385834	P1
ACSL3P1	ENST00000474389.1	n.483C>T		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42950 AN: 151990 Hom.: 6988 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.296

GnomAD4 exome AF: 0.170 AC: 1684 AN: 9926 Hom.: 166 Cov.: 0 AF XY: 0.168 AC XY: 928 AN XY: 5538

Gnomad4 AFR exome AF: 0.0300

Gnomad4 AMR exome AF: 0.193

Gnomad4 ASJ exome AF: 0.142

Gnomad4 EAS exome AF: 0.204

Gnomad4 SAS exome AF: 0.154

Gnomad4 FIN exome AF: 0.200

Gnomad4 NFE exome AF: 0.145

Gnomad4 OTH exome AF: 0.171

GnomAD4 genome AF: 0.283 AC: 42984 AN: 152108 Hom.: 6994 Cov.: 33 AF XY: 0.286 AC XY: 21257 AN XY: 74360

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.298

Alfa AF: 0.309 Hom.: 1480

Bravo AF: 0.281

Asia WGS AF: 0.393 AC: 1365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	5.2
DANN	Benign	0.61
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs8177248; hg19: chr3-133479626;