rs777818463

Variant names:

• chr10-29291962-C-A
• rs777818463
• NM_032517.6:c.95C>A

Your query was ambiguous. Multiple possible variants found:

• chr10-29291962-C-A
• chr10-29291962-C-G
• chr10-29291962-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_032517.6(LYZL1):​c.95C>A​(p.Ser32*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000317 in 1,578,494 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0000071 (0 hom., cov: 23)
  • Exomes 𝑓: 0.0000028 (0 hom.)
• Consequence: LYZL1 NM_032517.6 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LYZL1	NM_032517.6	c.95C>A	p.Ser32*	stop_gained	Exon 2 of 5	ENST00000649382.2	NP_115906.4
LYZL1	XM_005252627.4	c.233C>A	p.Ser78*	stop_gained	Exon 2 of 5		XP_005252684.1
LYZL1	XM_017016791.2	c.233C>A	p.Ser78*	stop_gained	Exon 2 of 5		XP_016872280.1
LYZL1	XR_428650.2	n.281C>A		non_coding_transcript_exon_variant	Exon 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LYZL1	ENST00000649382.2	c.95C>A	p.Ser32*	stop_gained	Exon 2 of 5		NM_032517.6	ENSP00000498092.1
LYZL1	ENST00000375500.8	c.233C>A	p.Ser78*	stop_gained	Exon 2 of 5	1		ENSP00000364650.3
LYZL1	ENST00000494304.1	n.38C>A		non_coding_transcript_exon_variant	Exon 1 of 5	3		ENSP00000434629.1

Frequencies

GnomAD3 genomes AF: 0.00000706 AC: 1 AN: 141550 Hom.: 0 Cov.: 23

Gnomad AFR AF: 0.0000255

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000133 AC: 3 AN: 224966 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 120812

Gnomad AFR exome AF: 0.0000643

Gnomad AMR exome AF: 0.0000618

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000278 AC: 4 AN: 1436944 Hom.: 0 Cov.: 34 AF XY: 0.00000140 AC XY: 1 AN XY: 713014

Gnomad4 AFR exome AF: 0.0000602

Gnomad4 AMR exome AF: 0.0000462

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000706 AC: 1 AN: 141550 Hom.: 0 Cov.: 23 AF XY: 0.0000146 AC XY: 1 AN XY: 68582

Gnomad4 AFR AF: 0.0000255

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.20	D
BayesDel_noAF	Pathogenic	0.24
CADD	Pathogenic	34
DANN	Uncertain	0.99
Eigen	Benign	0.17
Eigen_PC	Benign	-0.18
FATHMM_MKL	Benign	0.017	N
Vest4		0.050
GERP RS		1.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs777818463; hg19: chr10-29580891;