3-46465599-CTTTT-CTT

Position:

• chr3-46465599-CTTTT-CTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001321122.2(LTF):​c.4+2651_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 0.13 (1735 hom., cov: 0)
• 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 Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LTF	NM_001321122.2	c.4+2651_4+2652del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LTF	ENST00000443496.5	c.4+2651_4+2652del		intron_variant		2
LTF	ENST00000498301.1	c.4+2651_4+2652del		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19052 AN: 149322 Hom.: 1724 Cov.: 0

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.0466

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0405

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0590

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0555

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.128 AC: 19112 AN: 149404 Hom.: 1735 Cov.: 0 AF XY: 0.131 AC XY: 9519 AN XY: 72762

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.0405

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0590

Gnomad4 NFE AF: 0.0555

Gnomad4 OTH AF: 0.119

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;