3-46465599-CTTTT-CTT

Variant names:

• chr3-46465599-CTT-C
• rs5848800
• NM_001321122.2:c.4+2651_4+2652delAA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001321122.2(LTF):​c.4+2651_4+2652delAA 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
• 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: Benign. The variant received -8 ACMG points.

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

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+2651_4+2652delAA		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+2651_4+2652delAA		intron	N/A	ENSP00000397427.1
	LTF	ENST00000498301.1	TSL:4	c.4+2651_4+2652delAA		intron	N/A	ENSP00000508000.1

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

African (AFR) AF: 0.237 AC: 9633 AN: 40664

American (AMR) AF: 0.200 AC: 3020 AN: 15092

Ashkenazi Jewish (ASJ) AF: 0.0405 AC: 140 AN: 3454

East Asian (EAS) AF: 0.223 AC: 1141 AN: 5128

South Asian (SAS) AF: 0.117 AC: 557 AN: 4754

European-Finnish (FIN) AF: 0.0590 AC: 575 AN: 9746

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0555 AC: 3738 AN: 67304

Other (OTH) AF: 0.119 AC: 245 AN: 2066

Alfa AF: 0.0391 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;