X-153694714-C-T

Variant summary

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

The NM_005629.4(SLC6A8):​c.1597-5C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,209,202 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 16 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.000071 ( 0 hom., 4 hem., cov: 25)
Exomes 𝑓: 0.000034 ( 0 hom. 12 hem. )

Consequence

SLC6A8
NM_005629.4 splice_region, splice_polypyrimidine_tract, intron

Scores

2
Splicing: ADA: 0.0001377
2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.11
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant X-153694714-C-T is Benign according to our data. Variant chrX-153694714-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 416000.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High Hemizygotes in GnomAd4 at 4 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC6A8NM_005629.4 linkuse as main transcriptc.1597-5C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant ENST00000253122.10
SLC6A8NM_001142805.2 linkuse as main transcriptc.1567-5C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
SLC6A8NM_001142806.1 linkuse as main transcriptc.1252-5C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC6A8ENST00000253122.10 linkuse as main transcriptc.1597-5C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 NM_005629.4 P1P48029-1
SLC6A8ENST00000430077.6 linkuse as main transcriptc.1252-5C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 2 P48029-4
SLC6A8ENST00000485324.1 linkuse as main transcriptn.1904-5C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.0000712
AC:
8
AN:
112419
Hom.:
0
Cov.:
25
AF XY:
0.000116
AC XY:
4
AN XY:
34615
show subpopulations
Gnomad AFR
AF:
0.000162
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000281
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000376
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000104
AC:
19
AN:
182328
Hom.:
0
AF XY:
0.0000741
AC XY:
5
AN XY:
67492
show subpopulations
Gnomad AFR exome
AF:
0.000459
Gnomad AMR exome
AF:
0.000402
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000725
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000123
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000337
AC:
37
AN:
1096732
Hom.:
0
Cov.:
38
AF XY:
0.0000331
AC XY:
12
AN XY:
362796
show subpopulations
Gnomad4 AFR exome
AF:
0.000341
Gnomad4 AMR exome
AF:
0.000284
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000331
Gnomad4 SAS exome
AF:
0.0000185
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000154
Gnomad4 OTH exome
AF:
0.0000652
GnomAD4 genome
AF:
0.0000711
AC:
8
AN:
112470
Hom.:
0
Cov.:
25
AF XY:
0.000115
AC XY:
4
AN XY:
34676
show subpopulations
Gnomad4 AFR
AF:
0.000161
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000282
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000376
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000945

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Creatine transporter deficiency Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJan 28, 2024- -
SLC6A8-related disorder Benign:1
Likely benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesDec 04, 2019This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxJun 23, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
0.15
DANN
Benign
0.50

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.00014
dbscSNV1_RF
Benign
0.18
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.

Other links and lift over

dbSNP: rs376073223; hg19: chrX-152960169; API