10-29293319-T-C

Variant names:

• chr10-29293319-T-C
• rs1774950
• NM_032517.6:c.298+642T>C

Variant summary

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

The NM_032517.6(LYZL1):​c.298+642T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 151,322 control chromosomes in the GnomAD database, including 20,010 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 0.51 (20010 hom., cov: 28)
• Consequence: LYZL1 NM_032517.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.06
• Publications: 3 publications found

Genes affected

LYZL1 (HGNC:30502): (lysozyme like 1) Predicted to enable lysozyme activity. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000305098 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032517.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LYZL1	NM_032517.6	MANE Select	c.298+642T>C		intron	N/A	NP_115906.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LYZL1	ENST00000649382.2	MANE Select	c.298+642T>C		intron	N/A	ENSP00000498092.1
	LYZL1	ENST00000375500.8	TSL:1	c.436+642T>C		intron	N/A	ENSP00000364650.3
	LYZL1	ENST00000494304.1	TSL:3	n.241+642T>C		intron	N/A	ENSP00000434629.1

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76727 AN: 151208 Hom.: 19998 Cov.: 28

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.507 AC: 76778 AN: 151322 Hom.: 20010 Cov.: 28 AF XY: 0.505 AC XY: 37304 AN XY: 73902

African (AFR) AF: 0.368 AC: 15201 AN: 41318

American (AMR) AF: 0.539 AC: 8194 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1878 AN: 3466

East Asian (EAS) AF: 0.534 AC: 2716 AN: 5086

South Asian (SAS) AF: 0.518 AC: 2476 AN: 4780

European-Finnish (FIN) AF: 0.534 AC: 5549 AN: 10396

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39092 AN: 67784

Other (OTH) AF: 0.523 AC: 1096 AN: 2096

Alfa AF: 0.551 Hom.: 98441

Bravo AF: 0.499

Asia WGS AF: 0.516 AC: 1795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.37
PhyloP100		-3.1
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: rs1774950; hg19: chr10-29582248;