chr10-29292015-C-A

Position:

• chr10-29292015-C-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_032517.6(LYZL1):​c.139+9C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 1,101,922 control chromosomes in the GnomAD database, including 59,101 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.28 (4769 hom., cov: 19)
  • Exomes 𝑓: 0.16 (54332 hom.)
• Consequence: LYZL1 NM_032517.6 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0280

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 10-29292015-C-A is Benign according to our data. Variant chr10-29292015-C-A is described in ClinVar as [Benign]. Clinvar id is 769367.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LYZL1	NM_032517.6	c.139+9C>A		intron_variant		ENST00000649382.2
LYZL1	XM_005252627.4	c.277+9C>A		intron_variant
LYZL1	XM_017016791.2	c.277+9C>A		intron_variant
LYZL1	XR_428650.2	n.325+9C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LYZL1	ENST00000649382.2	c.139+9C>A		intron_variant			NM_032517.6	P1
LYZL1	ENST00000375500.8	c.277+9C>A		intron_variant		1
LYZL1	ENST00000494304.1	c.82+9C>A		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.280 AC: 24585 AN: 87924 Hom.: 4770 Cov.: 19

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.301

GnomAD3 exomes AF: 0.0402 AC: 6738 AN: 167764 Hom.: 2778 AF XY: 0.0384 AC XY: 3482 AN XY: 90590

Gnomad AFR exome AF: 0.0198

Gnomad AMR exome AF: 0.0453

Gnomad ASJ exome AF: 0.0273

Gnomad EAS exome AF: 0.112

Gnomad SAS exome AF: 0.0297

Gnomad FIN exome AF: 0.0239

Gnomad NFE exome AF: 0.0378

Gnomad OTH exome AF: 0.0571

GnomAD4 exome AF: 0.160 AC: 161809 AN: 1013952 Hom.: 54332 Cov.: 33 AF XY: 0.165 AC XY: 83253 AN XY: 504362

Gnomad4 AFR exome AF: 0.0900

Gnomad4 AMR exome AF: 0.218

Gnomad4 ASJ exome AF: 0.284

Gnomad4 EAS exome AF: 0.430

Gnomad4 SAS exome AF: 0.194

Gnomad4 FIN exome AF: 0.291

Gnomad4 NFE exome AF: 0.133

Gnomad4 OTH exome AF: 0.216

GnomAD4 genome AF: 0.279 AC: 24582 AN: 87970 Hom.: 4769 Cov.: 19 AF XY: 0.266 AC XY: 11252 AN XY: 42320

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.299

Alfa AF: 0.444 Hom.: 2271

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 15, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.5
DANN	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1774948; hg19: chr10-29580944; COSMIC: COSV64966946;