17-58244090-GACACACACACACACACACACACACACACAC-GACACACACACACACACACACAC

Variant names:

• chr17-58244090-GACACACAC-G
• rs67390833
• NM_006151.3:c.164+44_164+51delACACACAC

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_006151.3(LPO):​c.164+44_164+51delACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00586 in 1,058,936 control chromosomes in the GnomAD database, including 15 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0068 (2 hom., cov: 0)
  • Exomes 𝑓: 0.0057 (13 hom.)
• Consequence: LPO NM_006151.3 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: Likely_benign. The variant received -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006151.3. 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+44_164+51delACACACAC		intron	N/A	NP_006142.1
	LPO	NM_001160102.2		c.76+1070_76+1077delACACACAC		intron	N/A	NP_001153574.1
	LPO	NR_027647.2		n.234+1070_234+1077delACACACAC		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+44_164+51delACACACAC		intron	N/A	ENSP00000262290.4
	LPO	ENST00000421678.6	TSL:1	c.76+1070_76+1077delACACACAC		intron	N/A	ENSP00000400245.2
	LPO	ENST00000578403.5	TSL:1	n.235+44_235+51delACACACAC		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00678 AC: 955 AN: 140878 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.00703

Gnomad AMI AF: 0.00113

Gnomad AMR AF: 0.00672

Gnomad ASJ AF: 0.0158

Gnomad EAS AF: 0.000633

Gnomad SAS AF: 0.00272

Gnomad FIN AF: 0.0169

Gnomad MID AF: 0.0101

Gnomad NFE AF: 0.00556

Gnomad OTH AF: 0.00680

GnomAD4 exome AF: 0.00572 AC: 5253 AN: 917958 Hom.: 13 AF XY: 0.00577 AC XY: 2727 AN XY: 472410

African (AFR) AF: 0.00835 AC: 177 AN: 21208

American (AMR) AF: 0.00410 AC: 160 AN: 39006

Ashkenazi Jewish (ASJ) AF: 0.0136 AC: 298 AN: 21980

East Asian (EAS) AF: 0.00140 AC: 50 AN: 35838

South Asian (SAS) AF: 0.00277 AC: 200 AN: 72092

European-Finnish (FIN) AF: 0.0138 AC: 565 AN: 40846

Middle Eastern (MID) AF: 0.0124 AC: 55 AN: 4436

European-Non Finnish (NFE) AF: 0.00549 AC: 3517 AN: 640162

Other (OTH) AF: 0.00545 AC: 231 AN: 42390

GnomAD4 genome AF: 0.00677 AC: 954 AN: 140978 Hom.: 2 Cov.: 0 AF XY: 0.00680 AC XY: 464 AN XY: 68196

African (AFR) AF: 0.00701 AC: 261 AN: 37248

American (AMR) AF: 0.00672 AC: 95 AN: 14146

Ashkenazi Jewish (ASJ) AF: 0.0158 AC: 53 AN: 3362

East Asian (EAS) AF: 0.000634 AC: 3 AN: 4732

South Asian (SAS) AF: 0.00273 AC: 12 AN: 4398

European-Finnish (FIN) AF: 0.0169 AC: 153 AN: 9060

Middle Eastern (MID) AF: 0.0109 AC: 3 AN: 276

European-Non Finnish (NFE) AF: 0.00554 AC: 360 AN: 64934

Other (OTH) AF: 0.00672 AC: 13 AN: 1934

Alfa AF: 0.00 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

Splicing

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

Other links and lift over

dbSNP: rs67390833; hg19: chr17-56321451;