rs373858466

Variant names:

• chr10-29292001-G-A
• NM_032517.6:c.134G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-29292001-G-A
• chr10-29292001-G-T

Variant summary

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

The NM_032517.6(LYZL1):​c.134G>A​(p.Gly45Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000861 in 1,161,096 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G45V) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 23)
  • Exomes 𝑓: 8.6e-7 (0 hom.)
• Consequence: LYZL1 NM_032517.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62

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.134G>A	p.Gly45Glu	missense_variant	Exon 2 of 5	ENST00000649382.2	NP_115906.4
LYZL1	XM_005252627.4	c.272G>A	p.Gly91Glu	missense_variant	Exon 2 of 5		XP_005252684.1
LYZL1	XM_017016791.2	c.272G>A	p.Gly91Glu	missense_variant	Exon 2 of 5		XP_016872280.1
LYZL1	XR_428650.2	n.320G>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.134G>A	p.Gly45Glu	missense_variant	Exon 2 of 5		NM_032517.6	ENSP00000498092.1
LYZL1	ENST00000375500.8	c.272G>A	p.Gly91Glu	missense_variant	Exon 2 of 5	1		ENSP00000364650.3
LYZL1	ENST00000494304.1	n.77G>A		non_coding_transcript_exon_variant	Exon 1 of 5	3		ENSP00000434629.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome AF: 8.61e-7 AC: 1 AN: 1161096 Hom.: 0 Cov.: 34 AF XY: 0.00000172 AC XY: 1 AN XY: 581006

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000211

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.41
BayesDel_addAF	Uncertain	0.11	D
BayesDel_noAF	Uncertain	-0.070
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.10	.;T
Eigen	Benign	0.15
Eigen_PC	Benign	0.21
FATHMM_MKL	Uncertain	0.81	D
LIST_S2	Benign	0.77	T;T
M_CAP	Benign	0.030	D
MetaRNN	Uncertain	0.63	D;D
MetaSVM	Benign	-0.81	T
MutationAssessor	Benign	1.0	.;L
PrimateAI	Uncertain	0.64	T
PROVEAN	Uncertain	-2.8	D;.
REVEL	Uncertain	0.43
Sift	Benign	0.064	T;.
Sift4G	Benign	0.15	T;.
Polyphen		0.85	P;.
Vest4		0.76
MutPred		0.67		Gain of solvent accessibility (P = 0.0411);.;
MVP		0.76
MPC		0.23
ClinPred		0.94	D
GERP RS		3.6
Varity_R		0.32
gMVP		0.70

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-29580930; COSMIC: COSV64966447;