NM_001321122.2:c.4+2652delA

Variant names:

• chr3-46465599-CT-C
• rs5848800
• NM_001321122.2:c.4+2652delA

Variant summary

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

The NM_001321122.2(LTF):​c.4+2652delA 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
• 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 (SAS) allele frequency at 95% confidence interval = 0.146 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+2652delA		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+2652delA		intron	N/A	ENSP00000397427.1
	LTF	ENST00000498301.1	TSL:4	c.4+2652delA		intron	N/A	ENSP00000508000.1

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

African (AFR) AF: 0.0242 AC: 985 AN: 40700

American (AMR) AF: 0.0345 AC: 522 AN: 15112

Ashkenazi Jewish (ASJ) AF: 0.0553 AC: 191 AN: 3456

East Asian (EAS) AF: 0.0766 AC: 393 AN: 5128

South Asian (SAS) AF: 0.155 AC: 737 AN: 4758

European-Finnish (FIN) AF: 0.146 AC: 1423 AN: 9746

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 290

European-Non Finnish (NFE) AF: 0.0771 AC: 5189 AN: 67292

Other (OTH) AF: 0.0523 AC: 108 AN: 2066

Alfa AF: 0.0738 Hom.: 721

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.87

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;