X-153695062-CCT-CCTCT
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_005629.4(SLC6A8):c.1768-8_1768-7dupTC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000066 in 1,196,663 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 25 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000035 ( 0 hom., 1 hem., cov: 23)
Exomes 𝑓: 0.000069 ( 0 hom. 24 hem. )
Consequence
SLC6A8
NM_005629.4 splice_region, intron
NM_005629.4 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.00700
Publications
0 publications found
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 Gene-Disease associations (from GenCC):
- creatine transporter deficiencyInheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, ClinGen, Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -6 ACMG points.
BP6
Variant X-153695062-C-CCT is Benign according to our data. Variant chrX-153695062-C-CCT is described in ClinVar as Likely_benign. ClinVar VariationId is 1583949.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Hemizygotes in GnomAdExome4 at 24 XL gene
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SLC6A8 | NM_005629.4 | c.1768-8_1768-7dupTC | splice_region_variant, intron_variant | Intron 12 of 12 | ENST00000253122.10 | NP_005620.1 | ||
| SLC6A8 | NM_001142805.2 | c.1738-8_1738-7dupTC | splice_region_variant, intron_variant | Intron 12 of 12 | NP_001136277.1 | |||
| SLC6A8 | NM_001142806.1 | c.1423-8_1423-7dupTC | splice_region_variant, intron_variant | Intron 12 of 12 | NP_001136278.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SLC6A8 | ENST00000253122.10 | c.1768-12_1768-11insCT | intron_variant | Intron 12 of 12 | 1 | NM_005629.4 | ENSP00000253122.5 | |||
| SLC6A8 | ENST00000430077.6 | c.1423-12_1423-11insCT | intron_variant | Intron 12 of 12 | 2 | ENSP00000403041.2 | ||||
| SLC6A8 | ENST00000485324.1 | n.2075-12_2075-11insCT | intron_variant | Intron 5 of 5 | 2 |
Frequencies
GnomAD3 genomes 0.0000355 AC: 4AN: 112688Hom.: 0 Cov.: 23 show subpopulations
GnomAD3 genomes
AF:
AC:
4
AN:
112688
Hom.:
Cov.:
23
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
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Gnomad EAS
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Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.0000192 AC: 3AN: 156096 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
3
AN:
156096
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000692 AC: 75AN: 1083975Hom.: 0 Cov.: 31 AF XY: 0.0000679 AC XY: 24AN XY: 353255 show subpopulations
GnomAD4 exome
AF:
AC:
75
AN:
1083975
Hom.:
Cov.:
31
AF XY:
AC XY:
24
AN XY:
353255
show subpopulations
African (AFR)
AF:
AC:
0
AN:
26147
American (AMR)
AF:
AC:
0
AN:
34010
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
19027
East Asian (EAS)
AF:
AC:
0
AN:
29642
South Asian (SAS)
AF:
AC:
0
AN:
52082
European-Finnish (FIN)
AF:
AC:
0
AN:
39269
Middle Eastern (MID)
AF:
AC:
0
AN:
3742
European-Non Finnish (NFE)
AF:
AC:
70
AN:
834594
Other (OTH)
AF:
AC:
5
AN:
45462
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.488
Heterozygous variant carriers
0
3
6
9
12
15
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
4
8
12
16
20
<30
30-35
35-40
40-45
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50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.0000355 AC: 4AN: 112688Hom.: 0 Cov.: 23 AF XY: 0.0000287 AC XY: 1AN XY: 34846 show subpopulations
GnomAD4 genome
AF:
AC:
4
AN:
112688
Hom.:
Cov.:
23
AF XY:
AC XY:
1
AN XY:
34846
show subpopulations
African (AFR)
AF:
AC:
0
AN:
30977
American (AMR)
AF:
AC:
0
AN:
10765
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2658
East Asian (EAS)
AF:
AC:
0
AN:
3581
South Asian (SAS)
AF:
AC:
0
AN:
2749
European-Finnish (FIN)
AF:
AC:
0
AN:
6285
Middle Eastern (MID)
AF:
AC:
0
AN:
239
European-Non Finnish (NFE)
AF:
AC:
4
AN:
53242
Other (OTH)
AF:
AC:
0
AN:
1512
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Creatine transporter deficiency Benign:1
Aug 28, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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