chr3-133789620-A-T

Variant names:

• chr3-133789620-A-T
• rs1830084
• NM_001063.4:c.*11000A>T

Variant summary

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

The NM_001063.4(TF):​c.*11000A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,174 control chromosomes in the GnomAD database, including 7,080 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 0.29 (7079 hom., cov: 33)
  • Exomes 𝑓: 0.25 (1 hom.)
• Consequence: TF NM_001063.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

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]

SRPRB (HGNC:24085): (SRP receptor subunit beta) The protein encoded by this gene has similarity to mouse protein which is a subunit of the signal recognition particle receptor (SR). This subunit is a transmembrane GTPase belonging to the GTPase superfamily. It anchors alpha subunit, a peripheral membrane GTPase, to the ER membrane. SR is required for the cotranslational targeting of both secretory and membrane proteins to the ER membrane. [provided by RefSeq, Jul 2008]

LOC105374116 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TF	NM_001063.4	c.*11000A>T		3_prime_UTR_variant	Exon 17 of 17	ENST00000402696.9	NP_001054.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TF	ENST00000402696.9	c.*11000A>T		3_prime_UTR_variant	Exon 17 of 17	1	NM_001063.4	ENSP00000385834.3
SRPRB	ENST00000466490.7	c.-174+5476A>T		intron_variant	Intron 1 of 7	5		ENSP00000418401.1

Frequencies

GnomAD3 genomes AF: 0.289 AC: 44004 AN: 152036 Hom.: 7060 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.294

GnomAD4 exome AF: 0.250 AC: 5 AN: 20 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 FIN exome AF: 0.250

GnomAD4 genome AF: 0.290 AC: 44053 AN: 152154 Hom.: 7079 Cov.: 33 AF XY: 0.292 AC XY: 21751 AN XY: 74386

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.300

Alfa AF: 0.173 Hom.: 359

Bravo AF: 0.293

Asia WGS AF: 0.411 AC: 1428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.96
DANN	Benign	0.16

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: rs1830084; hg19: chr3-133508464;