10-29293319-T-C

Position:

• chr10-29293319-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LYZL1	NM_032517.6	c.298+642T>C		intron_variant		ENST00000649382.2
LYZL1	XM_005252627.4	c.436+642T>C		intron_variant
LYZL1	XM_017016791.2	c.436+642T>C		intron_variant
LYZL1	XR_428650.2	n.484+642T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LYZL1	ENST00000649382.2	c.298+642T>C		intron_variant			NM_032517.6	P1
LYZL1	ENST00000375500.8	c.436+642T>C		intron_variant		1
LYZL1	ENST00000494304.1	c.241+642T>C		intron_variant, NMD_transcript_variant		3

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

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.523

Alfa AF: 0.559 Hom.: 48695

Bravo AF: 0.499

Asia WGS AF: 0.516 AC: 1795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.37

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: rs1774950; hg19: chr10-29582248;