3-46465599-CTTTT-CT

Variant names:

• chr3-46465599-CTTT-C
• rs5848800
• NM_001321122.2:c.4+2650_4+2652delAAA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001321122.2(LTF):​c.4+2650_4+2652delAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.59 (25741 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: LTF NM_001321122.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001321122.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LTF	NM_001321122.2		c.4+2650_4+2652delAAA		intron	N/A	NP_001308051.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LTF	ENST00000443496.5	TSL:2	c.4+2650_4+2652delAAA		intron	N/A	ENSP00000397427.1
	LTF	ENST00000498301.1	TSL:4	c.4+2650_4+2652delAAA		intron	N/A	ENSP00000508000.1

Frequencies

GnomAD3 genomes AF: 0.586 AC: 87593 AN: 149372 Hom.: 25732 Cov.: 0

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.618

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.586 AC: 87638 AN: 149456 Hom.: 25741 Cov.: 0 AF XY: 0.585 AC XY: 42546 AN XY: 72772

African (AFR) AF: 0.500 AC: 20344 AN: 40670

American (AMR) AF: 0.580 AC: 8757 AN: 15104

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2383 AN: 3456

East Asian (EAS) AF: 0.689 AC: 3537 AN: 5130

South Asian (SAS) AF: 0.639 AC: 3036 AN: 4754

European-Finnish (FIN) AF: 0.591 AC: 5779 AN: 9784

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.621 AC: 41788 AN: 67302

Other (OTH) AF: 0.612 AC: 1260 AN: 2060

Alfa AF: 0.498 Hom.: 721

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs5848800; hg19: chr3-46507089;