17-58244090-GACACACACACACACACACACACACACACAC-GACACACACACACACACACACACACACAC

Variant names:

• chr17-58244090-GAC-G
• rs67390833
• NM_006151.3:c.164+50_164+51delAC

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6 BA1

The NM_006151.3(LPO):​c.164+50_164+51delAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.08 in 1,036,622 control chromosomes in the GnomAD database, including 649 homozygotes. Variant has been reported in Lovd as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.081 (481 hom., cov: 0)
  • Exomes 𝑓: 0.080 (168 hom.)
• Consequence: LPO NM_006151.3 intron
• Clinical Significance: Not reported in ClinVar
• 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]

ENSG00000286788 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP6: Variant 17-58244090-GAC-G is Benign according to our data. Variant chr17-58244090-GAC-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LPO	NM_006151.3	c.164+50_164+51delAC		intron_variant	Intron 3 of 12	ENST00000262290.9	NP_006142.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPO	ENST00000262290.9	c.164+50_164+51delAC		intron_variant	Intron 3 of 12	1	NM_006151.3	ENSP00000262290.4

Frequencies

GnomAD3 genomes AF: 0.0812 AC: 11430 AN: 140690 Hom.: 480 Cov.: 0

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0968

Gnomad AMR AF: 0.0704

Gnomad ASJ AF: 0.0983

Gnomad EAS AF: 0.0720

Gnomad SAS AF: 0.0842

Gnomad FIN AF: 0.0451

Gnomad MID AF: 0.128

Gnomad NFE AF: 0.0711

Gnomad OTH AF: 0.0891

GnomAD3 exomes AF: 0.110 AC: 15071 AN: 136960 Hom.: 32 AF XY: 0.111 AC XY: 8145 AN XY: 73692

Gnomad AFR exome AF: 0.104

Gnomad AMR exome AF: 0.103

Gnomad ASJ exome AF: 0.119

Gnomad EAS exome AF: 0.154

Gnomad SAS exome AF: 0.119

Gnomad FIN exome AF: 0.0741

Gnomad NFE exome AF: 0.106

Gnomad OTH exome AF: 0.115

GnomAD4 exome AF: 0.0798 AC: 71447 AN: 895836 Hom.: 168 AF XY: 0.0823 AC XY: 37902 AN XY: 460642

Gnomad4 AFR exome AF: 0.0887

Gnomad4 AMR exome AF: 0.0931

Gnomad4 ASJ exome AF: 0.125

Gnomad4 EAS exome AF: 0.165

Gnomad4 SAS exome AF: 0.108

Gnomad4 FIN exome AF: 0.0783

Gnomad4 NFE exome AF: 0.0683

Gnomad4 OTH exome AF: 0.0935

GnomAD4 genome AF: 0.0813 AC: 11442 AN: 140786 Hom.: 481 Cov.: 0 AF XY: 0.0797 AC XY: 5428 AN XY: 68108

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0703

Gnomad4 ASJ AF: 0.0983

Gnomad4 EAS AF: 0.0720

Gnomad4 SAS AF: 0.0847

Gnomad4 FIN AF: 0.0451

Gnomad4 NFE AF: 0.0711

Gnomad4 OTH AF: 0.0887

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		Details are displayed if max score is > 0.2

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;