Genetic Variant LYZL4:p.Phe53Phe (chr3-42406979-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.204

Publications

16 publications found

Variant links:

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]

LYZL4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LYZL4	NM_144634.4 link	c.159C>T	p.Phe53Phe	synonymous_variant	Exon 3 of 5	ENST00000287748.8	NP_653235.1	Q96KX0A0A080YUZ5
LYZL4	NM_001304386.2 link	c.159C>T	p.Phe53Phe	synonymous_variant	Exon 3 of 5		NP_001291315.1	Q96KX0A0A080YUZ5
LYZL4	XM_011533355.4 link	c.159C>T	p.Phe53Phe	synonymous_variant	Exon 3 of 5		XP_011531657.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
LYZL4	ENST00000287748.8 link	c.159C>T	p.Phe53Phe	synonymous_variant	Exon 3 of 5	1	NM_144634.4	ENSP00000287748.3	Q96KX0
LYZL4	ENST00000441172.1 link	c.159C>T	p.Phe53Phe	synonymous_variant	Exon 3 of 5	5		ENSP00000387897.1	Q96KX0
LYZL4	ENST00000470991.1 link	n.189C>T		non_coding_transcript_exon_variant	Exon 3 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.0813

AC:

12371

AN:

152084

Hom.:

748

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.106

AC XY:

76840

AN XY:

727234

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

7850

15699

23549

31398

39248

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4308

8616

12924

17232

21540

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0813

AC:

12370

AN:

152202

Hom.:

748

Cov.:

AF XY:

0.0861

AC XY:

6402

AN XY:

74388

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.0973

AC:

6618

AN:

68004

Other (OTH)

AF:

0.0663

AC:

140

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

561

1123

1684

2246

2807

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

320

480

640

800

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

7.5

(source)

DANN

Benign

0.73

PhyloP100

-0.20

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over