15-44651559-A-G

Position:

chr15-44651559-A-G

Variant summary

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

The NM_025137.4(SPG11):c.1388T>C(p.Phe463Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 1,613,660 control chromosomes in the GnomAD database, including 167,750 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.48 ( 17741 hom., cov: 32)

Exomes 𝑓: 0.45 ( 150009 hom. )

Consequence

SPG11
NM_025137.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:15

Conservation

PhyloP100: 1.39

Variant links:

Genes affected

SPG11 (HGNC:11226): (SPG11 vesicle trafficking associated, spatacsin) The protein encoded by this gene is a potential transmembrane protein that is phosphorylated upon DNA damage. Defects in this gene are a cause of spastic paraplegia type 11 (SPG11). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]

SPG11 links:

SPG11 (HGNC:):

SPG11 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=4.9492717E-4).

BP6

Variant 15-44651559-A-G is Benign according to our data. Variant chr15-44651559-A-G is described in ClinVar as [Benign]. Clinvar id is 41271.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-44651559-A-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPG11	NM_025137.4 linkuse as main transcript	c.1388T>C	p.Phe463Ser	missense_variant	6/40	ENST00000261866.12	NP_079413.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPG11	ENST00000261866.12 linkuse as main transcript	c.1388T>C	p.Phe463Ser	missense_variant	6/40	1	NM_025137.4	ENSP00000261866.7		Q96JI7-1

Frequencies

GnomAD3 genomes

AF:

0.481

AC:

73026

AN:

151916

Hom.:

17722

Cov.:

show subpopulations

Gnomad AFR

AF:

0.524

Gnomad AMI

AF:

0.595

Gnomad AMR

AF:

0.543

Gnomad ASJ

AF:

0.465

Gnomad EAS

AF:

0.482

Gnomad SAS

AF:

0.368

Gnomad FIN

AF:

0.481

Gnomad MID

AF:

0.446

Gnomad NFE

AF:

0.448

Gnomad OTH

AF:

0.473

GnomAD3 exomes

AF:

0.468

AC:

117565

AN:

251374

Hom.:

28019

AF XY:

0.458

AC XY:

62202

AN XY:

135856

show subpopulations

Gnomad AFR exome

AF:

0.528

Gnomad AMR exome

AF:

0.568

Gnomad ASJ exome

AF:

0.462

Gnomad EAS exome

AF:

0.456

Gnomad SAS exome

AF:

0.371

Gnomad FIN exome

AF:

0.482

Gnomad NFE exome

AF:

0.454

Gnomad OTH exome

AF:

0.469

GnomAD4 exome

AF:

0.451

AC:

659493

AN:

1461626

Hom.:

150009

Cov.:

AF XY:

0.449

AC XY:

326424

AN XY:

727136

show subpopulations

Gnomad4 AFR exome

AF:

0.524

Gnomad4 AMR exome

AF:

0.569

Gnomad4 ASJ exome

AF:

0.464

Gnomad4 EAS exome

AF:

0.541

Gnomad4 SAS exome

AF:

0.368

Gnomad4 FIN exome

AF:

0.492

Gnomad4 NFE exome

AF:

0.446

Gnomad4 OTH exome

AF:

0.450

GnomAD4 genome

AF:

0.481

AC:

73084

AN:

152034

Hom.:

17741

Cov.:

AF XY:

0.480

AC XY:

35695

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.523

Gnomad4 AMR

AF:

0.543

Gnomad4 ASJ

AF:

0.465

Gnomad4 EAS

AF:

0.482

Gnomad4 SAS

AF:

0.367

Gnomad4 FIN

AF:

0.481

Gnomad4 NFE

AF:

0.448

Gnomad4 OTH

AF:

0.473

Alfa

AF:

0.454

Hom.:

40099

Bravo

AF:

0.490

TwinsUK

AF:

0.437

AC:

1622

ALSPAC

AF:

0.435

AC:

1678

ESP6500AA

AF:

0.525

AC:

2310

ESP6500EA

AF:

0.456

AC:

3917

ExAC

AF:

0.466

AC:

56539

Asia WGS

AF:

0.462

AC:

1607

AN:

3478

EpiCase

AF:

0.445

EpiControl

AF:

0.454

ClinVar

Significance: Benign

Submissions summary: Benign:15

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Hereditary spastic paraplegia 11

Benign:7

Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	Apr 22, 2016	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Apr 13, 2017	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	-	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
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. -
Benign, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

not specified

Benign:4

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	Clinical Genetics, Academic Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 21, 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. -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -

Hereditary spastic paraplegia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome Diagnostics Laboratory, The Hospital for Sick Children

Dec 12, 2016

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Amyotrophic lateral sclerosis type 5

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

- -

Charcot-Marie-Tooth disease axonal type 2X

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.32

BayesDel_addAF

Benign

-0.42

BayesDel_noAF

Benign

-0.24

CADD

Benign

DANN

Benign

0.96

DEOGEN2

Benign

0.039

T;.;T;.;.

Eigen

Benign

-0.37

Eigen_PC

Benign

-0.26

FATHMM_MKL

Benign

0.14

LIST_S2

Benign

0.81

T;T;T;T;T

MetaRNN

Benign

0.00049

T;T;T;T;T

MetaSVM

Benign

-0.90

MutationAssessor

Uncertain

2.1

M;M;.;M;.

PrimateAI

Benign

0.42

PROVEAN

Benign

-1.3

N;N;N;N;N

REVEL

Benign

0.18

Sift

Benign

0.34

T;T;T;T;T

Sift4G

Benign

0.33

T;T;T;T;T

Polyphen

0.021

B;.;B;.;.

Vest4

0.20

MPC

0.30

ClinPred

0.016

GERP RS

4.9

Varity_R

0.096

gMVP

0.40

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