rs201526436

Positions:

chrX-153694553-G-A

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_005629.4(SLC6A8):c.1516G>A(p.Asp506Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000381 in 1,207,138 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 151 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. D506D) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.00036 ( 0 hom., 8 hem., cov: 23)

Exomes 𝑓: 0.00038 ( 0 hom. 143 hem. )

Consequence

SLC6A8
NM_005629.4 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 1.44

Variant links:

Genes affected

SLC6A8 (HGNC:11055): (solute carrier family 6 member 8) The protein encoded by this gene is a plasma membrane protein whose function is to transport creatine into and out of cells. Defects in this gene can result in X-linked creatine deficiency syndrome. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

SLC6A8 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.022884935).

BP6

Variant X-153694553-G-A is Benign according to our data. Variant chrX-153694553-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 287609.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-153694553-G-A is described in Lovd as [Benign]. Variant chrX-153694553-G-A is described in Lovd as [Likely_benign].

BS2

High Hemizygotes in GnomAd4 at 8 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
SLC6A8	NM_005629.4 linkuse as main transcript	c.1516G>A	p.Asp506Asn	missense_variant	11/13	ENST00000253122.10
SLC6A8	NM_001142805.2 linkuse as main transcript	c.1486G>A	p.Asp496Asn	missense_variant	11/13
SLC6A8	NM_001142806.1 linkuse as main transcript	c.1171G>A	p.Asp391Asn	missense_variant	11/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC6A8	ENST00000253122.10 linkuse as main transcript	c.1516G>A	p.Asp506Asn	missense_variant	11/13	1	NM_005629.4	P1	P48029-1
SLC6A8	ENST00000430077.6 linkuse as main transcript	c.1171G>A	p.Asp391Asn	missense_variant	11/13	2			P48029-4
SLC6A8	ENST00000413787.1 linkuse as main transcript	c.445G>A	p.Asp149Asn	missense_variant	6/6	5
SLC6A8	ENST00000485324.1 linkuse as main transcript	n.1823G>A		non_coding_transcript_exon_variant	4/6	2

Frequencies

GnomAD3 genomes

AF:

0.000363

AC:

AN:

110228

Hom.:

Cov.:

AF XY:

0.000246

AC XY:

AN XY:

32502

show subpopulations

Gnomad AFR

AF:

0.0000994

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00380

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000170

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000494

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000459

AC:

AN:

183109

Hom.:

AF XY:

0.000501

AC XY:

AN XY:

67813

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000365

Gnomad ASJ exome

AF:

0.00240

Gnomad EAS exome

AF:

0.0000722

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000750

Gnomad NFE exome

AF:

0.000625

Gnomad OTH exome

AF:

0.000221

GnomAD4 exome

AF:

0.000383

AC:

420

AN:

1096910

Hom.:

Cov.:

AF XY:

0.000395

AC XY:

143

AN XY:

362434

show subpopulations

Gnomad4 AFR exome

AF:

0.0000379

Gnomad4 AMR exome

AF:

0.0000284

Gnomad4 ASJ exome

AF:

0.00258

Gnomad4 EAS exome

AF:

0.0000994

Gnomad4 SAS exome

AF:

0.0000185

Gnomad4 FIN exome

AF:

0.000618

Gnomad4 NFE exome

AF:

0.000385

Gnomad4 OTH exome

AF:

0.000326

GnomAD4 genome

AF:

0.000363

AC:

AN:

110228

Hom.:

Cov.:

AF XY:

0.000246

AC XY:

AN XY:

32502

show subpopulations

Gnomad4 AFR

AF:

0.0000994

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00380

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000170

Gnomad4 NFE

AF:

0.000494

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000669

Hom.:

Bravo

AF:

0.000321

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000892

AC:

ExAC

AF:

0.000461

AC:

EpiCase

AF:

0.000327

EpiControl

AF:

0.000652

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 23, 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, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	May 02, 2016	- -
Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	May 19, 2016	- -

Creatine transporter deficiency

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 29, 2024

- -

Inborn genetic diseases

Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

May 31, 2017

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2024

SLC6A8: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.49

BayesDel_addAF

Benign

-0.41

BayesDel_noAF

Benign

-0.44

CADD

Benign

DANN

Benign

0.48

DEOGEN2

Benign

0.16

T;.;.

FATHMM_MKL

Uncertain

0.95

LIST_S2

Uncertain

0.95

D;D;D

M_CAP

Pathogenic

0.29

MetaRNN

Benign

0.023

T;T;T

MetaSVM

Benign

-0.82

MutationAssessor

Benign

1.4

L;.;.

MutationTaster

Benign

1.0

D;D

PrimateAI

Uncertain

0.53

PROVEAN

Benign

0.70

N;N;N

REVEL

Benign

0.23

Sift

Benign

1.0

T;T;T

Sift4G

Benign

1.0

T;T;T

Polyphen

0.048

B;.;.

Vest4

0.24

MVP

0.60

MPC

0.36

ClinPred

0.030

GERP RS

4.8

Varity_R

0.19

gMVP

0.97

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