17-58244090-GACAC-G

Variant names:

• chr17-58244090-GACAC-G
• rs67390833
• NM_006151.3:c.164+48_164+51delACAC

Variant summary

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

The ENST00000262290.9(LPO):​c.164+48_164+51delACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 1,049,340 control chromosomes in the GnomAD database, including 5,643 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.22 (3519 hom., cov: 0)
  • Exomes 𝑓: 0.14 (2124 hom.)
• Consequence: LPO ENST00000262290.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000262290.9. 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
	LPO	NM_006151.3	MANE Select	c.164+48_164+51delACAC		intron	N/A	NP_006142.1
	LPO	NM_001160102.2		c.76+1074_76+1077delACAC		intron	N/A	NP_001153574.1
	LPO	NR_027647.2		n.234+1074_234+1077delACAC		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPO	ENST00000262290.9	TSL:1 MANE Select	c.164+48_164+51delACAC		intron	N/A	ENSP00000262290.4
	LPO	ENST00000421678.6	TSL:1	c.76+1074_76+1077delACAC		intron	N/A	ENSP00000400245.2
	LPO	ENST00000578403.5	TSL:1	n.235+48_235+51delACAC		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.222 AC: 31221 AN: 140668 Hom.: 3519 Cov.: 0

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.0486

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.265

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.233

GnomAD2 exomes AF: 0.168 AC: 23042 AN: 136960 AF XY: 0.171

Gnomad AFR exome AF: 0.143

Gnomad AMR exome AF: 0.124

Gnomad ASJ exome AF: 0.188

Gnomad EAS exome AF: 0.0579

Gnomad FIN exome AF: 0.185

Gnomad NFE exome AF: 0.211

Gnomad OTH exome AF: 0.184

GnomAD4 exome AF: 0.140 AC: 127344 AN: 908572 Hom.: 2124 AF XY: 0.144 AC XY: 67207 AN XY: 467390

African (AFR) AF: 0.125 AC: 2614 AN: 20994

American (AMR) AF: 0.110 AC: 4227 AN: 38378

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 3820 AN: 21604

East Asian (EAS) AF: 0.0570 AC: 1991 AN: 34902

South Asian (SAS) AF: 0.128 AC: 9065 AN: 71066

European-Finnish (FIN) AF: 0.201 AC: 8120 AN: 40448

Middle Eastern (MID) AF: 0.158 AC: 692 AN: 4378

European-Non Finnish (NFE) AF: 0.142 AC: 90136 AN: 634964

Other (OTH) AF: 0.160 AC: 6679 AN: 41838

GnomAD4 genome AF: 0.222 AC: 31238 AN: 140768 Hom.: 3519 Cov.: 0 AF XY: 0.217 AC XY: 14781 AN XY: 68072

African (AFR) AF: 0.176 AC: 6530 AN: 37200

American (AMR) AF: 0.203 AC: 2865 AN: 14126

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 812 AN: 3358

East Asian (EAS) AF: 0.0487 AC: 230 AN: 4726

South Asian (SAS) AF: 0.154 AC: 674 AN: 4388

European-Finnish (FIN) AF: 0.239 AC: 2154 AN: 9028

Middle Eastern (MID) AF: 0.261 AC: 72 AN: 276

European-Non Finnish (NFE) AF: 0.266 AC: 17229 AN: 64850

Other (OTH) AF: 0.231 AC: 445 AN: 1928

Alfa AF: 0.191 Hom.: 254

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs67390833; hg19: chr17-56321451;