dbSNP rs4525863: TF:c.-90+4111C>A (chr3-133717292-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001354703.2(TF):c.-90+4111C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,954 control chromosomes in the GnomAD database, including 8,196 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 ( 8196 hom., cov: 31)

Consequence

TF
NM_001354703.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04

Variant links:

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 links:

ENSG00000291042 (HGNC:):

ENSG00000291042 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TF	NM_001354703.2 link	c.-90+4111C>A		intron_variant	Intron 7 of 22		NP_001341632.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291042	ENST00000460564.5 link	n.381+16239C>A		intron_variant	Intron 3 of 4	4

Frequencies

GnomAD3 genomes

AF:

0.324

AC:

49191

AN:

151836

Hom.:

8194

Cov.:

show subpopulations

Gnomad AFR

AF:

0.316

Gnomad AMI

AF:

0.263

Gnomad AMR

AF:

0.363

Gnomad ASJ

AF:

0.244

Gnomad EAS

AF:

0.416

Gnomad SAS

AF:

0.414

Gnomad FIN

AF:

0.306

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.316

Gnomad OTH

AF:

0.301

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.324

AC:

49218

AN:

151954

Hom.:

8196

Cov.:

AF XY:

0.326

AC XY:

24211

AN XY:

74254

show subpopulations

Gnomad4 AFR

AF:

0.316

Gnomad4 AMR

AF:

0.364

Gnomad4 ASJ

AF:

0.244

Gnomad4 EAS

AF:

0.415

Gnomad4 SAS

AF:

0.413

Gnomad4 FIN

AF:

0.306

Gnomad4 NFE

AF:

0.316

Gnomad4 OTH

AF:

0.301

Alfa

AF:

0.315

Hom.:

15539

Bravo

AF:

0.327

Asia WGS

AF:

0.432

AC:

1501

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.6

DANN

Benign

0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over