rs5848800

Variant names:

• chr3-46465599-CTTTT-C
• rs5848800
• NM_001321122.2:c.4+2649_4+2652delAAAA

Your query was ambiguous. Multiple possible variants found:

• chr3-46465599-CTTTT-C
• chr3-46465599-CTTTT-CT
• chr3-46465599-CTTTT-CTT
• chr3-46465599-CTTTT-CTTT
• chr3-46465599-CTTTT-CTTTTT
• chr3-46465599-CTTTT-CTTTTTT
• chr3-46465599-CTTTT-CTTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001321122.2(LTF):​c.4+2649_4+2652delAAAA 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 0.00067 (0 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: Uncertain_significance. The variant received 0 ACMG points.

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+2649_4+2652delAAAA		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+2649_4+2652delAAAA		intron	N/A	ENSP00000397427.1
	LTF	ENST00000498301.1	TSL:4	c.4+2649_4+2652delAAAA		intron	N/A	ENSP00000508000.1

Frequencies

GnomAD3 genomes AF: 0.000670 AC: 100 AN: 149320 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000370

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00106

Gnomad ASJ AF: 0.000579

Gnomad EAS AF: 0.00117

Gnomad SAS AF: 0.000419

Gnomad FIN AF: 0.00134

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.000550

Gnomad OTH AF: 0.00195

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

GnomAD4 genome AF: 0.000669 AC: 100 AN: 149404 Hom.: 0 Cov.: 0 AF XY: 0.000783 AC XY: 57 AN XY: 72758

African (AFR) AF: 0.000393 AC: 16 AN: 40702

American (AMR) AF: 0.00106 AC: 16 AN: 15094

Ashkenazi Jewish (ASJ) AF: 0.000579 AC: 2 AN: 3454

East Asian (EAS) AF: 0.00117 AC: 6 AN: 5130

South Asian (SAS) AF: 0.000421 AC: 2 AN: 4756

European-Finnish (FIN) AF: 0.00134 AC: 13 AN: 9726

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.000550 AC: 37 AN: 67280

Other (OTH) AF: 0.00194 AC: 4 AN: 2066

Alfa AF: 0.000393 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;