3-42406979-G-A

Position:

• chr3-42406979-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_144634.4(LYZL4):​c.159C>T​(p.Phe53=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,614,052 control chromosomes in the GnomAD database, including 10,181 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.081 (748 hom., cov: 31)
  • Exomes 𝑓: 0.10 (9433 hom.)
• Consequence: LYZL4 NM_144634.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204

Genes affected

LYZL4 (HGNC:28387): (lysozyme like 4) Lysozymes (see LYZ; MIM 153450), especially C-type lysozymes, are well-recognized bacteriolytic factors widely distributed in the animal kingdom and play a mainly protective role in host defense. LYZL4 is a member of a family of lysozyme-like genes (Zhang et al., 2005 [PubMed 16014814]).[supplied by OMIM, Apr 2009]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BP7: Synonymous conserved (PhyloP=-0.204 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LYZL4	NM_144634.4	c.159C>T	p.Phe53=	synonymous_variant	3/5	ENST00000287748.8
LYZL4	NM_001304386.2	c.159C>T	p.Phe53=	synonymous_variant	3/5
LYZL4	XM_011533355.4	c.159C>T	p.Phe53=	synonymous_variant	3/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LYZL4	ENST00000287748.8	c.159C>T	p.Phe53=	synonymous_variant	3/5	1	NM_144634.4	P1
LYZL4	ENST00000441172.1	c.159C>T	p.Phe53=	synonymous_variant	3/5	5		P1
LYZL4	ENST00000470991.1	n.189C>T		non_coding_transcript_exon_variant	3/5	3

Frequencies

GnomAD3 genomes AF: 0.0813 AC: 12371 AN: 152084 Hom.: 748 Cov.: 31

Gnomad AFR AF: 0.0219

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0624

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0973

Gnomad OTH AF: 0.0656

GnomAD3 exomes AF: 0.103 AC: 25876 AN: 251382 Hom.: 1890 AF XY: 0.106 AC XY: 14417 AN XY: 135864

Gnomad AFR exome AF: 0.0202

Gnomad AMR exome AF: 0.0553

Gnomad ASJ exome AF: 0.0377

Gnomad EAS exome AF: 0.292

Gnomad SAS exome AF: 0.127

Gnomad FIN exome AF: 0.122

Gnomad NFE exome AF: 0.0951

Gnomad OTH exome AF: 0.0867

GnomAD4 exome AF: 0.105 AC: 153407 AN: 1461850 Hom.: 9433 Cov.: 35 AF XY: 0.106 AC XY: 76840 AN XY: 727234

Gnomad4 AFR exome AF: 0.0180

Gnomad4 AMR exome AF: 0.0535

Gnomad4 ASJ exome AF: 0.0372

Gnomad4 EAS exome AF: 0.295

Gnomad4 SAS exome AF: 0.130

Gnomad4 FIN exome AF: 0.122

Gnomad4 NFE exome AF: 0.102

Gnomad4 OTH exome AF: 0.103

GnomAD4 genome AF: 0.0813 AC: 12370 AN: 152202 Hom.: 748 Cov.: 31 AF XY: 0.0861 AC XY: 6402 AN XY: 74388

Gnomad4 AFR AF: 0.0218

Gnomad4 AMR AF: 0.0626

Gnomad4 ASJ AF: 0.0363

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.0973

Gnomad4 OTH AF: 0.0663

Alfa AF: 0.0945 Hom.: 1564

Bravo AF: 0.0734

Asia WGS AF: 0.197 AC: 685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	7.5
DANN	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs2286720; hg19: chr3-42448471; COSMIC: COSV55104821;