Variant rs5848800 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001321122.2(LTF):c.4+2649_4+2652del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000669 in 149,404 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00067 ( 0 hom., cov: 0)

Consequence

LTF
NM_001321122.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.148

Variant links:

Genes affected

LTF (HGNC:6720): (lactotransferrin) This gene is a member of the transferrin family of genes and its protein product is found in the secondary granules of neutrophils. The protein is a major iron-binding protein in milk and body secretions with an antimicrobial activity, making it an important component of the non-specific immune system. The protein demonstrates a broad spectrum of properties, including regulation of iron homeostasis, host defense against a broad range of microbial infections, anti-inflammatory activity, regulation of cellular growth and differentiation and protection against cancer development and metastasis. Antimicrobial, antiviral, antifungal and antiparasitic activity has been found for this protein and its peptides. Activity against both DNA and RNA viruses has been found, including activity against SARS-CoV-2, and HIV. [provided by RefSeq, Jul 2021]

LTF links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LTF	NM_001321122.2 linkuse as main transcript	c.4+2649_4+2652del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LTF	ENST00000443496.5 linkuse as main transcript	c.4+2649_4+2652del		intron_variant		2
LTF	ENST00000498301.1 linkuse as main transcript	c.4+2649_4+2652del		intron_variant		4

Frequencies

GnomAD3 genomes

AF:

0.000670

AC:

100

AN:

149320

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000370

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00106

Gnomad ASJ

AF:

0.000579

Gnomad EAS

AF:

0.00117

Gnomad SAS

AF:

0.000419

Gnomad FIN

AF:

0.00134

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.000550

Gnomad OTH

AF:

0.00195

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

GnomAD4 genome

AF:

0.000669

AC:

100

AN:

149404

Hom.:

Cov.:

AF XY:

0.000783

AC XY:

AN XY:

72758

show subpopulations

Gnomad4 AFR

AF:

0.000393

Gnomad4 AMR

AF:

0.00106

Gnomad4 ASJ

AF:

0.000579

Gnomad4 EAS

AF:

0.00117

Gnomad4 SAS

AF:

0.000421

Gnomad4 FIN

AF:

0.00134

Gnomad4 NFE

AF:

0.000550

Gnomad4 OTH

AF:

0.00194

Alfa

AF:

0.000393

Hom.:

721

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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