14-67786135-A-T

Variant summary

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

The NM_015346.4(ZFYVE26):c.3118T>A(p.Ser1040Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0452 in 1,614,158 control chromosomes in the GnomAD database, including 2,189 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 0.039 ( 204 hom., cov: 32)

Exomes 𝑓: 0.046 ( 1985 hom. )

Consequence

ZFYVE26
NM_015346.4 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.344

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=0.0017139316).

BP6

Variant 14-67786135-A-T is Benign according to our data. Variant chr14-67786135-A-T is described in ClinVar as [Benign]. Clinvar id is 130778.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-67786135-A-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZFYVE26	NM_015346.4 linkuse as main transcript	c.3118T>A	p.Ser1040Thr	missense_variant	17/42	ENST00000347230.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZFYVE26	ENST00000347230.9 linkuse as main transcript	c.3118T>A	p.Ser1040Thr	missense_variant	17/42	1	NM_015346.4	P1

Frequencies

GnomAD3 genomes

AF:

0.0393

AC:

5985

AN:

152172

Hom.:

204

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00934

Gnomad AMI

AF:

0.00989

Gnomad AMR

AF:

0.112

Gnomad ASJ

AF:

0.00663

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0114

Gnomad FIN

AF:

0.0306

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0497

Gnomad OTH

AF:

0.0445

GnomAD3 exomes

AF:

0.0494

AC:

12416

AN:

251448

Hom.:

637

AF XY:

0.0445

AC XY:

6052

AN XY:

135894

show subpopulations

Gnomad AFR exome

AF:

0.00849

Gnomad AMR exome

AF:

0.160

Gnomad ASJ exome

AF:

0.00774

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0112

Gnomad FIN exome

AF:

0.0308

Gnomad NFE exome

AF:

0.0475

Gnomad OTH exome

AF:

0.0420

GnomAD4 exome

AF:

0.0458

AC:

66978

AN:

1461868

Hom.:

1985

Cov.:

AF XY:

0.0445

AC XY:

32382

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.00726

Gnomad4 AMR exome

AF:

0.152

Gnomad4 ASJ exome

AF:

0.00807

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.0120

Gnomad4 FIN exome

AF:

0.0344

Gnomad4 NFE exome

AF:

0.0489

Gnomad4 OTH exome

AF:

0.0396

GnomAD4 genome

AF:

0.0393

AC:

5986

AN:

152290

Hom.:

204

Cov.:

AF XY:

0.0396

AC XY:

2952

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.00931

Gnomad4 AMR

AF:

0.112

Gnomad4 ASJ

AF:

0.00663

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.0114

Gnomad4 FIN

AF:

0.0306

Gnomad4 NFE

AF:

0.0497

Gnomad4 OTH

AF:

0.0441

Alfa

AF:

0.0451

Hom.:

166

Bravo

AF:

0.0435

TwinsUK

AF:

0.0485

AC:

180

ALSPAC

AF:

0.0441

AC:

170

ESP6500AA

AF:

0.00999

AC:

ESP6500EA

AF:

0.0420

AC:

361

ExAC

AF:

0.0444

AC:

5385

Asia WGS

AF:

0.00722

AC:

AN:

3478

EpiCase

AF:

0.0452

EpiControl

AF:

0.0404

ClinVar

Significance: Benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jun 06, 2012	- -
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, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 08, 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. -

Hereditary spastic paraplegia 15

Benign:4

Benign, criteria provided, single submitter	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	Oct 09, 2014	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Dec 05, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	Dec 10, 2014	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 12, 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

Invitae

Feb 01, 2024

- -

Hereditary spastic paraplegia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome Diagnostics Laboratory, The Hospital for Sick Children

Oct 30, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.077

BayesDel_addAF

Benign

-0.77

BayesDel_noAF

Benign

-0.74

Cadd

Benign

Dann

Benign

0.76

Eigen

Benign

-0.95

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.14

MetaRNN

Benign

0.0017

T;T

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.40

PROVEAN

Benign

-0.75

N;N

REVEL

Benign

0.016

Sift

Benign

0.21

T;T

Sift4G

Benign

0.41

T;T

Polyphen

0.15

.;B

Vest4

0.31

MPC

0.17

ClinPred

0.0033

GERP RS

-0.57

gMVP

0.12

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