rs3742884

Positions:

chr14-67785217-G-A

Variant summary

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

The NM_015346.4(ZFYVE26):c.3365C>T(p.Ala1122Val) variant causes a missense change. The variant allele was found at a frequency of 0.0219 in 1,613,908 control chromosomes in the GnomAD database, including 844 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.045 ( 315 hom., cov: 32)

Exomes 𝑓: 0.019 ( 529 hom. )

Consequence

ZFYVE26
NM_015346.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: 3.67

Variant links:

Genes affected

ZFYVE26 (HGNC:20761): (zinc finger FYVE-type containing 26) This gene encodes a protein which contains a FYVE zinc finger binding domain. The presence of this domain is thought to target these proteins to membrane lipids through interaction with phospholipids in the membrane. Mutations in this gene are associated with autosomal recessive spastic paraplegia-15. [provided by RefSeq, Oct 2008]

ZFYVE26 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 (MetaRNN=0.001244396).

BP6

Variant 14-67785217-G-A is Benign according to our data. Variant chr14-67785217-G-A is described in ClinVar as [Benign]. Clinvar id is 130781.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-67785217-G-A is described in Lovd as [Benign]. Variant chr14-67785217-G-A is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZFYVE26	NM_015346.4 linkuse as main transcript	c.3365C>T	p.Ala1122Val	missense_variant	19/42	ENST00000347230.9	NP_056161.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFYVE26	ENST00000347230.9 linkuse as main transcript	c.3365C>T	p.Ala1122Val	missense_variant	19/42	1	NM_015346.4	ENSP00000251119	P1

Frequencies

GnomAD3 genomes

AF:

0.0454

AC:

6914

AN:

152146

Hom.:

315

Cov.:

show subpopulations

Gnomad AFR

AF:

0.121

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0195

Gnomad ASJ

AF:

0.0115

Gnomad EAS

AF:

0.0515

Gnomad SAS

AF:

0.0195

Gnomad FIN

AF:

0.00885

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0150

Gnomad OTH

AF:

0.0421

GnomAD3 exomes

AF:

0.0246

AC:

6152

AN:

249942

Hom.:

178

AF XY:

0.0228

AC XY:

3080

AN XY:

135224

show subpopulations

Gnomad AFR exome

AF:

0.127

Gnomad AMR exome

AF:

0.0111

Gnomad ASJ exome

AF:

0.0107

Gnomad EAS exome

AF:

0.0516

Gnomad SAS exome

AF:

0.0182

Gnomad FIN exome

AF:

0.00806

Gnomad NFE exome

AF:

0.0161

Gnomad OTH exome

AF:

0.0195

GnomAD4 exome

AF:

0.0195

AC:

28484

AN:

1461644

Hom.:

529

Cov.:

AF XY:

0.0192

AC XY:

13992

AN XY:

727090

show subpopulations

Gnomad4 AFR exome

AF:

0.119

Gnomad4 AMR exome

AF:

0.0114

Gnomad4 ASJ exome

AF:

0.0114

Gnomad4 EAS exome

AF:

0.0602

Gnomad4 SAS exome

AF:

0.0194

Gnomad4 FIN exome

AF:

0.00929

Gnomad4 NFE exome

AF:

0.0157

Gnomad4 OTH exome

AF:

0.0238

GnomAD4 genome

AF:

0.0455

AC:

6927

AN:

152264

Hom.:

315

Cov.:

AF XY:

0.0440

AC XY:

3275

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.121

Gnomad4 AMR

AF:

0.0195

Gnomad4 ASJ

AF:

0.0115

Gnomad4 EAS

AF:

0.0519

Gnomad4 SAS

AF:

0.0197

Gnomad4 FIN

AF:

0.00885

Gnomad4 NFE

AF:

0.0151

Gnomad4 OTH

AF:

0.0416

Alfa

AF:

0.0229

Hom.:

199

Bravo

AF:

0.0506

TwinsUK

AF:

0.0175

AC:

ALSPAC

AF:

0.0143

AC:

ESP6500AA

AF:

0.122

AC:

538

ESP6500EA

AF:

0.0159

AC:

137

ExAC

AF:

0.0275

AC:

3339

Asia WGS

AF:

0.0360

AC:

125

AN:

3478

EpiCase

AF:

0.0159

EpiControl

AF:

0.0180

ClinVar

Significance: Benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Likely benign, no assertion criteria provided	clinical testing	Genetic Services Laboratory, University of Chicago	-	Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 25, 2016	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Sep 30, 2017	- -
Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Hereditary spastic paraplegia 15

Benign:2

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Dec 05, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Spastic paraplegia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Hereditary spastic paraplegia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome Diagnostics Laboratory, The Hospital for Sick Children

Dec 12, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.093

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.64

CADD

Benign

DANN

Benign

0.14

DEOGEN2

Benign

0.0089

.;T

Eigen

Benign

-0.49

Eigen_PC

Benign

-0.38

FATHMM_MKL

Benign

0.64

LIST_S2

Benign

0.71

.;T

MetaRNN

Benign

0.0012

T;T

MetaSVM

Benign

-0.99

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.37

PROVEAN

Benign

0.39

N;N

REVEL

Benign

0.088

Sift

Benign

1.0

T;T

Sift4G

Benign

1.0

T;T

Polyphen

0.012

.;B

Vest4

0.083

MPC

0.17

ClinPred

0.0085

GERP RS

2.7

gMVP

0.087

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

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