3-46465599-CTTTT-CTTT

Position:

• chr3-46465599-CTTTT-CTTT

Variant summary

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

The NM_001321122.2(LTF):​c.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 0.065 (406 hom., cov: 0)
• Consequence: LTF NM_001321122.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.873

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 (SAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0648 AC: 9684 AN: 149368 Hom.: 406 Cov.: 0

Gnomad AFR AF: 0.0241

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0346

Gnomad ASJ AF: 0.0553

Gnomad EAS AF: 0.0768

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0771

Gnomad OTH AF: 0.0513

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

GnomAD4 genome AF: 0.0648 AC: 9679 AN: 149450 Hom.: 406 Cov.: 0 AF XY: 0.0698 AC XY: 5080 AN XY: 72766

Gnomad4 AFR AF: 0.0242

Gnomad4 AMR AF: 0.0345

Gnomad4 ASJ AF: 0.0553

Gnomad4 EAS AF: 0.0766

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.0771

Gnomad4 OTH AF: 0.0523

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;