Genetic Variant SLC6A8:c.-5A>C (chrX-153688570-A-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_005629.4(SLC6A8):c.-5A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 18)

Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )

Failed GnomAD Quality Control

Consequence

SLC6A8
NM_005629.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.25

Publications

7 publications found

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:

PNCK (HGNC:13415): (pregnancy up-regulated nonubiquitous CaM kinase) PNCK is a member of the calcium/calmodulin-dependent protein kinase family of protein serine/threonine kinases (see CAMK1; MIM 604998) (Gardner et al., 2000 [PubMed 10673339]).[supplied by OMIM, Mar 2008]

PNCK links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC6A8	NM_005629.4 link	c.-5A>C		5_prime_UTR_variant	Exon 1 of 13	ENST00000253122.10	NP_005620.1	P48029-1X5D9C4
SLC6A8	NM_001142805.2 link	c.-5A>C		5_prime_UTR_variant	Exon 1 of 13		NP_001136277.1	P48029Q59EV7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC6A8	ENST00000253122.10 link	c.-5A>C	5_prime_UTR_variant	Exon 1 of 13	1	NM_005629.4	ENSP00000253122.5	P48029-1
PNCK	ENST00000458354.5 link	c.-3+245T>G	intron_variant	Intron 1 of 3	3		ENSP00000401542.1	C9J2B9
PNCK	ENST00000480693.1 link	n.64+245T>G	intron_variant	Intron 1 of 3	5
SLC6A8	ENST00000476466.1 link	n.-153A>C	upstream_gene_variant		3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

908277

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

283771

African (AFR)

AF:

0.00

AC:

AN:

18261

American (AMR)

AF:

0.00

AC:

AN:

15357

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

13910

East Asian (EAS)

AF:

0.00

AC:

AN:

16577

South Asian (SAS)

AF:

0.00

AC:

AN:

38435

European-Finnish (FIN)

AF:

0.00

AC:

AN:

28565

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2284

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

739148

Other (OTH)

AF:

0.00

AC:

AN:

35740

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

5398

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

(source)

DANN

Benign

0.85

PhyloP100

2.3

PromoterAI

0.092

Neutral

(source)

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.2

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over