rs2286720

Variant names:

• chr3-42406979-G-A
• rs2286720
• NM_144634.4:c.159C>T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_144634.4(LYZL4):​c.159C>T​(p.Phe53Phe) 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
• Publications: 16 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144634.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LYZL4	NM_144634.4	MANE Select	c.159C>T	p.Phe53Phe	synonymous	Exon 3 of 5	NP_653235.1	Q96KX0
	LYZL4	NM_001304386.2		c.159C>T	p.Phe53Phe	synonymous	Exon 3 of 5	NP_001291315.1	Q96KX0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LYZL4	ENST00000287748.8	TSL:1 MANE Select	c.159C>T	p.Phe53Phe	synonymous	Exon 3 of 5	ENSP00000287748.3	Q96KX0
	LYZL4	ENST00000441172.1	TSL:5	c.159C>T	p.Phe53Phe	synonymous	Exon 3 of 5	ENSP00000387897.1	Q96KX0
	LYZL4	ENST00000470991.1	TSL:3	n.189C>T		non_coding_transcript_exon	Exon 3 of 5

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

GnomAD2 exomes AF: 0.103 AC: 25876 AN: 251382 AF XY: 0.106

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 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

African (AFR) AF: 0.0180 AC: 603 AN: 33480

American (AMR) AF: 0.0535 AC: 2394 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 972 AN: 26136

East Asian (EAS) AF: 0.295 AC: 11721 AN: 39700

South Asian (SAS) AF: 0.130 AC: 11206 AN: 86258

European-Finnish (FIN) AF: 0.122 AC: 6511 AN: 53416

Middle Eastern (MID) AF: 0.0758 AC: 437 AN: 5768

European-Non Finnish (NFE) AF: 0.102 AC: 113322 AN: 1111976

Other (OTH) AF: 0.103 AC: 6241 AN: 60394

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

African (AFR) AF: 0.0218 AC: 907 AN: 41546

American (AMR) AF: 0.0626 AC: 957 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0363 AC: 126 AN: 3472

East Asian (EAS) AF: 0.294 AC: 1520 AN: 5164

South Asian (SAS) AF: 0.125 AC: 604 AN: 4822

European-Finnish (FIN) AF: 0.129 AC: 1368 AN: 10582

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0973 AC: 6618 AN: 68004

Other (OTH) AF: 0.0663 AC: 140 AN: 2112

Alfa AF: 0.0898 Hom.: 2219

Bravo AF: 0.0734

Asia WGS AF: 0.197 AC: 685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	7.5
DANN	Benign	0.73
PhyloP100		-0.20
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2286720; hg19: chr3-42448471; COSMIC: COSV55104821;