Variant 10-29292595-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_032517.6(LYZL1):c.216T>C(p.Tyr72=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000612 in 1,614,106 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00053 ( 0 hom., cov: 33)

Exomes 𝑓: 0.00062 ( 6 hom. )

Consequence

LYZL1
NM_032517.6 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.03

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 -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 10-29292595-T-C is Benign according to our data. Variant chr10-29292595-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2640387.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.03 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
LYZL1	NM_032517.6 linkuse as main transcript	c.216T>C	p.Tyr72=	synonymous_variant	3/5	ENST00000649382.2
LYZL1	XM_005252627.4 linkuse as main transcript	c.354T>C	p.Tyr118=	synonymous_variant	3/5
LYZL1	XM_017016791.2 linkuse as main transcript	c.354T>C	p.Tyr118=	synonymous_variant	3/5
LYZL1	XR_428650.2 linkuse as main transcript	n.402T>C		non_coding_transcript_exon_variant	3/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LYZL1	ENST00000649382.2 linkuse as main transcript	c.216T>C	p.Tyr72=	synonymous_variant	3/5		NM_032517.6	P1	Q6UWQ5-1
LYZL1	ENST00000375500.8 linkuse as main transcript	c.354T>C	p.Tyr118=	synonymous_variant	3/5	1			Q6UWQ5-2
LYZL1	ENST00000494304.1 linkuse as main transcript	c.159T>C	p.Tyr53=	synonymous_variant, NMD_transcript_variant	2/5	3

Frequencies

GnomAD3 genomes

AF:

0.000525

AC:

AN:

152246

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000386

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000392

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000617

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.000684

AC:

172

AN:

251414

Hom.:

AF XY:

0.000751

AC XY:

102

AN XY:

135864

show subpopulations

Gnomad AFR exome

AF:

0.000369

Gnomad AMR exome

AF:

0.000347

Gnomad ASJ exome

AF:

0.00119

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.00160

Gnomad FIN exome

AF:

0.0000924

Gnomad NFE exome

AF:

0.000704

Gnomad OTH exome

AF:

0.00130

GnomAD4 exome

AF:

0.000621

AC:

908

AN:

1461742

Hom.:

Cov.:

AF XY:

0.000677

AC XY:

492

AN XY:

727148

show subpopulations

Gnomad4 AFR exome

AF:

0.000657

Gnomad4 AMR exome

AF:

0.000425

Gnomad4 ASJ exome

AF:

0.000919

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.00188

Gnomad4 FIN exome

AF:

0.0000562

Gnomad4 NFE exome

AF:

0.000544

Gnomad4 OTH exome

AF:

0.000861

GnomAD4 genome

AF:

0.000525

AC:

AN:

152364

Hom.:

Cov.:

AF XY:

0.000456

AC XY:

AN XY:

74512

show subpopulations

Gnomad4 AFR

AF:

0.000385

Gnomad4 AMR

AF:

0.000392

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000617

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.000716

Hom.:

Bravo

AF:

0.000574

EpiCase

AF:

0.00115

EpiControl

AF:

0.00124

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Aug 01, 2022

LYZL1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

0.66

DANN

Benign

0.35

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

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