10-30623101-G-T

Variant names:

• chr10-30623101-G-T
• rs399593
• NM_183058.3:c.298+3004C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_183058.3(LYZL2):​c.298+3004C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.856 in 152,210 control chromosomes in the GnomAD database, including 56,287 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 0.86 (56287 hom., cov: 32)
• Consequence: LYZL2 NM_183058.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 7 publications found

Genes affected

LYZL2 (HGNC:29613): (lysozyme like 2) 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. LYZL2 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LYZL2	NM_183058.3	c.298+3004C>A		intron_variant	Intron 3 of 4	ENST00000647634.2	NP_898881.3
LYZL2	XM_011519306.3	c.436+3004C>A		intron_variant	Intron 3 of 3		XP_011517608.1
LYZL2	XR_930469.3	n.484+3004C>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LYZL2	ENST00000647634.2	c.298+3004C>A		intron_variant	Intron 3 of 4		NM_183058.3	ENSP00000497408.1
LYZL2	ENST00000375318.4	c.436+3004C>A		intron_variant	Intron 3 of 4	1		ENSP00000364467.2

Frequencies

GnomAD3 genomes AF: 0.856 AC: 130180 AN: 152092 Hom.: 56250 Cov.: 32

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.854

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.856 AC: 130267 AN: 152210 Hom.: 56287 Cov.: 32 AF XY: 0.853 AC XY: 63502 AN XY: 74414

African (AFR) AF: 0.913 AC: 37920 AN: 41534

American (AMR) AF: 0.760 AC: 11615 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.847 AC: 2941 AN: 3472

East Asian (EAS) AF: 0.519 AC: 2681 AN: 5168

South Asian (SAS) AF: 0.749 AC: 3612 AN: 4820

European-Finnish (FIN) AF: 0.919 AC: 9741 AN: 10596

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.866 AC: 58923 AN: 68014

Other (OTH) AF: 0.855 AC: 1810 AN: 2116

Alfa AF: 0.858 Hom.: 103063

Bravo AF: 0.849

Asia WGS AF: 0.675 AC: 2347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.0
DANN	Benign	0.85
PhyloP100		0.23
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: rs399593; hg19: chr10-30912030;