3-46465599-CTTTT-CT

Position:

• chr3-46465599-CTTTT-CT

Variant summary

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

The NM_001321122.2(LTF):​c.4+2650_4+2652del 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

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LTF	NM_001321122.2	c.4+2650_4+2652del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LTF	ENST00000443496.5	c.4+2650_4+2652del		intron_variant		2
LTF	ENST00000498301.1	c.4+2650_4+2652del		intron_variant		4

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

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.612

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5848800; hg19: chr3-46507089;