Variant chr10-29292013-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_032517.6(LYZL1):c.139+7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 1,096,142 control chromosomes in the GnomAD database, including 60,598 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 4783 hom., cov: 19)

Exomes 𝑓: 0.16 ( 55815 hom. )

Consequence

LYZL1
NM_032517.6 splice_region, intron

Scores

Splicing: ADA: 0.0001034

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.191

Variant links:

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]

LYZL1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 10-29292013-C-T is Benign according to our data. Variant chr10-29292013-C-T is described in ClinVar as [Benign]. Clinvar id is 769366.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
LYZL1	NM_032517.6 linkuse as main transcript	c.139+7C>T	splice_region_variant, intron_variant	ENST00000649382.2
LYZL1	XM_005252627.4 linkuse as main transcript	c.277+7C>T	splice_region_variant, intron_variant
LYZL1	XM_017016791.2 linkuse as main transcript	c.277+7C>T	splice_region_variant, intron_variant
LYZL1	XR_428650.2 linkuse as main transcript	n.325+7C>T	splice_region_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
LYZL1	ENST00000649382.2 linkuse as main transcript	c.139+7C>T	splice_region_variant, intron_variant		NM_032517.6	P1	Q6UWQ5-1
LYZL1	ENST00000375500.8 linkuse as main transcript	c.277+7C>T	splice_region_variant, intron_variant	1			Q6UWQ5-2
LYZL1	ENST00000494304.1 linkuse as main transcript	c.82+7C>T	splice_region_variant, intron_variant, NMD_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.282

AC:

24725

AN:

87722

Hom.:

4784

Cov.:

show subpopulations

Gnomad AFR

AF:

0.165

Gnomad AMI

AF:

0.261

Gnomad AMR

AF:

0.314

Gnomad ASJ

AF:

0.349

Gnomad EAS

AF:

0.369

Gnomad SAS

AF:

0.259

Gnomad FIN

AF:

0.300

Gnomad MID

AF:

0.356

Gnomad NFE

AF:

0.351

Gnomad OTH

AF:

0.298

GnomAD3 exomes

AF:

0.0451

AC:

7585

AN:

168146

Hom.:

3172

AF XY:

0.0433

AC XY:

3933

AN XY:

90858

show subpopulations

Gnomad AFR exome

AF:

0.0218

Gnomad AMR exome

AF:

0.0533

Gnomad ASJ exome

AF:

0.0315

Gnomad EAS exome

AF:

0.126

Gnomad SAS exome

AF:

0.0325

Gnomad FIN exome

AF:

0.0247

Gnomad NFE exome

AF:

0.0423

Gnomad OTH exome

AF:

0.0655

GnomAD4 exome

AF:

0.165

AC:

165885

AN:

1008370

Hom.:

55815

Cov.:

AF XY:

0.170

AC XY:

85468

AN XY:

502094

show subpopulations

Gnomad4 AFR exome

AF:

0.0922

Gnomad4 AMR exome

AF:

0.223

Gnomad4 ASJ exome

AF:

0.291

Gnomad4 EAS exome

AF:

0.430

Gnomad4 SAS exome

AF:

0.199

Gnomad4 FIN exome

AF:

0.298

Gnomad4 NFE exome

AF:

0.138

Gnomad4 OTH exome

AF:

0.222

GnomAD4 genome

AF:

0.282

AC:

24725

AN:

87772

Hom.:

4783

Cov.:

AF XY:

0.268

AC XY:

11320

AN XY:

42188

show subpopulations

Gnomad4 AFR

AF:

0.164

Gnomad4 AMR

AF:

0.314

Gnomad4 ASJ

AF:

0.349

Gnomad4 EAS

AF:

0.368

Gnomad4 SAS

AF:

0.259

Gnomad4 FIN

AF:

0.300

Gnomad4 NFE

AF:

0.351

Gnomad4 OTH

AF:

0.297

Alfa

AF:

0.446

Hom.:

2283

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

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

3.1

DANN

Benign

0.50

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00010

dbscSNV1_RF

Benign

0.092

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over