NM_006151.3:c.164+48_164+51dupACAC

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_006151.3(LPO):​c.164+48_164+51dupACAC 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 0.072 (371 hom., cov: 0)
  • Exomes 𝑓: 0.035 (29 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LPO	NM_006151.3	c.164+48_164+51dupACAC		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+48_164+51dupACAC		intron_variant	Intron 3 of 12	1	NM_006151.3	ENSP00000262290.4

Frequencies

GnomAD3 genomes AF: 0.0721 AC: 10150 AN: 140740 Hom.: 372 Cov.: 0

Gnomad AFR AF: 0.0834

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.0631

Gnomad ASJ AF: 0.0351

Gnomad EAS AF: 0.0795

Gnomad SAS AF: 0.0492

Gnomad FIN AF: 0.0559

Gnomad MID AF: 0.0403

Gnomad NFE AF: 0.0722

Gnomad OTH AF: 0.0643

GnomAD3 exomes AF: 0.0455 AC: 6230 AN: 136960 Hom.: 35 AF XY: 0.0433 AC XY: 3194 AN XY: 73692

Gnomad AFR exome AF: 0.0551

Gnomad AMR exome AF: 0.0518

Gnomad ASJ exome AF: 0.0242

Gnomad EAS exome AF: 0.0698

Gnomad SAS exome AF: 0.0358

Gnomad FIN exome AF: 0.0318

Gnomad NFE exome AF: 0.0446

Gnomad OTH exome AF: 0.0443

GnomAD4 exome AF: 0.0351 AC: 32034 AN: 913648 Hom.: 29 Cov.: 0 AF XY: 0.0358 AC XY: 16820 AN XY: 470158

Gnomad4 AFR exome AF: 0.0520

Gnomad4 AMR exome AF: 0.0389

Gnomad4 ASJ exome AF: 0.0239

Gnomad4 EAS exome AF: 0.0754

Gnomad4 SAS exome AF: 0.0343

Gnomad4 FIN exome AF: 0.0409

Gnomad4 NFE exome AF: 0.0320

Gnomad4 OTH exome AF: 0.0383

GnomAD4 genome AF: 0.0721 AC: 10156 AN: 140840 Hom.: 371 Cov.: 0 AF XY: 0.0708 AC XY: 4821 AN XY: 68136

Gnomad4 AFR AF: 0.0832

Gnomad4 AMR AF: 0.0631

Gnomad4 ASJ AF: 0.0351

Gnomad4 EAS AF: 0.0793

Gnomad4 SAS AF: 0.0498

Gnomad4 FIN AF: 0.0559

Gnomad4 NFE AF: 0.0722

Gnomad4 OTH AF: 0.0646

ClinVar

Not reported in ClinVar

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;