17-58244090-G-GAC

Position:

• chr17-58244090-G-GAC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_006151.3(LPO):​c.164+50_164+51dupAC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.12 (1245 hom., cov: 0)
  • Exomes 𝑓: 0.049 (31 hom.)
• Consequence: LPO NM_006151.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.134

Genes affected

LPO (HGNC:6678): (lactoperoxidase) This gene encodes a member of the peroxidase family of proteins. The encoded preproprotein is proteolytically processed to generate the mature enzyme. Following its secretion from salivary, mammary, and other mucosal glands, this enzyme catalyzes the generation of the antimicrobial substance hypothiocyanous acid. This gene is present in a gene cluster on chromosome 17. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed. [provided by RefSeq, Jan 2016]

LPO (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 17-58244090-G-GAC is Benign according to our data. Variant chr17-58244090-G-GAC is described in ClinVar as [Benign]. Clinvar id is 403046.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPO	NM_006151.3	c.164+50_164+51dupAC		intron_variant		ENST00000262290.9	NP_006142.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LPO	ENST00000262290.9	c.164+50_164+51dupAC		intron_variant		1	NM_006151.3	ENSP00000262290.4

Frequencies

GnomAD3 genomes AF: 0.119 AC: 16715 AN: 140600 Hom.: 1239 Cov.: 0

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.0440

Gnomad EAS AF: 0.0839

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0935

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0763

Gnomad OTH AF: 0.110

GnomAD3 exomes AF: 0.0664 AC: 9099 AN: 136960 Hom.: 28 AF XY: 0.0644 AC XY: 4745 AN XY: 73692

Gnomad AFR exome AF: 0.158

Gnomad AMR exome AF: 0.0623

Gnomad ASJ exome AF: 0.0346

Gnomad EAS exome AF: 0.0804

Gnomad SAS exome AF: 0.0760

Gnomad FIN exome AF: 0.0598

Gnomad NFE exome AF: 0.0537

Gnomad OTH exome AF: 0.0679

GnomAD4 exome AF: 0.0487 AC: 44364 AN: 911362 Hom.: 31 Cov.: 0 AF XY: 0.0499 AC XY: 23427 AN XY: 469016

Gnomad4 AFR exome AF: 0.138

Gnomad4 AMR exome AF: 0.0494

Gnomad4 ASJ exome AF: 0.0346

Gnomad4 EAS exome AF: 0.0783

Gnomad4 SAS exome AF: 0.0759

Gnomad4 FIN exome AF: 0.0781

Gnomad4 NFE exome AF: 0.0389

Gnomad4 OTH exome AF: 0.0587

GnomAD4 genome AF: 0.119 AC: 16753 AN: 140700 Hom.: 1245 Cov.: 0 AF XY: 0.119 AC XY: 8067 AN XY: 68054

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.0849

Gnomad4 ASJ AF: 0.0440

Gnomad4 EAS AF: 0.0843

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0935

Gnomad4 NFE AF: 0.0763

Gnomad4 OTH AF: 0.112

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

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: rs67390833; hg19: chr17-56321451;