Genetic Variant LYST:p.Thr3Thr (chr1-235830409-G-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2

The NM_000081.4(LYST):c.9C>T(p.Thr3Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0154 in 1,611,378 control chromosomes in the GnomAD database, including 220 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.011 ( 8 hom., cov: 32)

Exomes 𝑓: 0.016 ( 212 hom. )

Consequence

LYST
NM_000081.4 synonymous

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:6

Conservation

PhyloP100: -0.148

Publications

6 publications found

Variant links:

Genes affected

LYST (HGNC:1968): (lysosomal trafficking regulator) This gene encodes a protein that regulates intracellular protein trafficking in endosomes, and may be involved in pigmentation. Mutations in this gene are associated with Chediak-Higashi syndrome, a lysosomal storage disorder. Alternative splicing results in multiple transcript variants, though the full-length nature of some of these variants has not been determined. [provided by RefSeq, Apr 2013]

LYST Gene-Disease associations (from GenCC):

Chediak-Higashi syndrome
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet, ClinGen, Genomics England PanelApp
attenuated Chédiak-Higashi syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

LYST links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant 1-235830409-G-A is Benign according to our data. Variant chr1-235830409-G-A is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 254942.

BP7

Synonymous conserved (PhyloP=-0.148 with no splicing effect.

BS1

Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0115 (1745/151914) while in subpopulation AMR AF = 0.0184 (280/15250). AF 95% confidence interval is 0.0166. There are 8 homozygotes in GnomAd4. There are 794 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 8 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000081.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
LYST	NM_000081.4	MANE Select	c.9C>T	p.Thr3Thr	synonymous	Exon 3 of 53	NP_000072.2	Q99698-1
LYST	NM_001301365.1		c.9C>T	p.Thr3Thr	synonymous	Exon 3 of 53	NP_001288294.1	Q99698-1
LYST	NR_102436.3		n.633C>T		non_coding_transcript_exon	Exon 3 of 4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
LYST	ENST00000389793.7	TSL:5 MANE Select	c.9C>T	p.Thr3Thr	synonymous	Exon 3 of 53	ENSP00000374443.2	Q99698-1
LYST	ENST00000468626.2	TSL:1	c.9C>T	p.Thr3Thr	synonymous	Exon 3 of 3	ENSP00000513173.1	A0A8V8TKS8
LYST	ENST00000468107.5	TSL:1	c.9C>T	p.Thr3Thr	synonymous	Exon 3 of 4	ENSP00000513172.1	A0A8V8TMC0

Frequencies

GnomAD3 genomes

AF:

0.0115

AC:

1746

AN:

151796

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00283

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0184

Gnomad ASJ

AF:

0.0185

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00312

Gnomad FIN

AF:

0.00723

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0168

Gnomad OTH

AF:

0.0226

GnomAD2 exomes

AF:

0.0115

AC:

2859

AN:

249432

AF XY:

0.0116

show subpopulations

Gnomad AFR exome

AF:

0.00229

Gnomad AMR exome

AF:

0.0118

Gnomad ASJ exome

AF:

0.0180

Gnomad EAS exome

AF:

0.000164

Gnomad FIN exome

AF:

0.00704

Gnomad NFE exome

AF:

0.0171

Gnomad OTH exome

AF:

0.0155

GnomAD4 exome

AF:

0.0158

AC:

23033

AN:

1459464

Hom.:

212

Cov.:

AF XY:

0.0154

AC XY:

11159

AN XY:

726150

show subpopulations

African (AFR)

AF:

0.00240

AC:

AN:

33348

American (AMR)

AF:

0.0129

AC:

576

AN:

44558

Ashkenazi Jewish (ASJ)

AF:

0.0184

AC:

479

AN:

26082

East Asian (EAS)

AF:

0.000101

AC:

AN:

39632

South Asian (SAS)

AF:

0.00295

AC:

254

AN:

86012

European-Finnish (FIN)

AF:

0.00806

AC:

430

AN:

53378

Middle Eastern (MID)

AF:

0.00991

AC:

AN:

5752

European-Non Finnish (NFE)

AF:

0.0182

AC:

20201

AN:

1110408

Other (OTH)

AF:

0.0158

AC:

952

AN:

60294

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.455

Heterozygous variant carriers

984

1968

2952

3936

4920

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

762

1524

2286

3048

3810

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0115

AC:

1745

AN:

151914

Hom.:

Cov.:

AF XY:

0.0107

AC XY:

794

AN XY:

74234

show subpopulations

African (AFR)

AF:

0.00282

AC:

117

AN:

41428

American (AMR)

AF:

0.0184

AC:

280

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.0185

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5182

South Asian (SAS)

AF:

0.00313

AC:

AN:

4798

European-Finnish (FIN)

AF:

0.00723

AC:

AN:

10516

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0168

AC:

1143

AN:

67964

Other (OTH)

AF:

0.0224

AC:

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

182

273

364

455

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0138

Hom.:

Bravo

AF:

0.0127

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.0163

EpiControl

AF:

0.0170

ClinVar

ClinVar submissions

Significance:Conflicting classifications of pathogenicity

Revision:criteria provided, conflicting classifications

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (3)

Chédiak-Higashi syndrome (2)

Autoinflammatory syndrome (1)

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

1.5

(source)

DANN

Benign

0.85

PhyloP100

-0.15

Mutation Taster

=100/0

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over