rs151335200

Variant names:

• chrX-153694552-C-A
• rs151335200
• NM_005629.4:c.1515C>A

Your query was ambiguous. Multiple possible variants found:

• chrX-153694552-C-A
• chrX-153694552-C-G
• chrX-153694552-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_005629.4(SLC6A8):​c.1515C>A​(p.Asp505Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000907 in 110,276 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. 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: 𝑓 0.0000091 (0 hom., 0 hem., cov: 22)
• Consequence: SLC6A8 NM_005629.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.75

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.23056585).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC6A8	NM_005629.4	c.1515C>A	p.Asp505Glu	missense_variant	Exon 11 of 13	ENST00000253122.10	NP_005620.1
SLC6A8	NM_001142805.2	c.1485C>A	p.Asp495Glu	missense_variant	Exon 11 of 13		NP_001136277.1
SLC6A8	NM_001142806.1	c.1170C>A	p.Asp390Glu	missense_variant	Exon 11 of 13		NP_001136278.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC6A8	ENST00000253122.10	c.1515C>A	p.Asp505Glu	missense_variant	Exon 11 of 13	1	NM_005629.4	ENSP00000253122.5

Frequencies

GnomAD3 genomes AF: 0.00000907 AC: 1 AN: 110276 Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0 AN XY: 32530

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000190

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 34

GnomAD4 genome AF: 0.00000907 AC: 1 AN: 110276 Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0 AN XY: 32530

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000190

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000378

ExAC AF: 0.00000824 AC: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.44
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Benign	-0.52
CADD	Benign	0.070
DANN	Benign	0.97
DEOGEN2	Uncertain	0.42	T;.;.
FATHMM_MKL	Benign	0.17	N
LIST_S2	Uncertain	0.91	D;D;D
M_CAP	Uncertain	0.20	D
MetaRNN	Benign	0.23	T;T;T
MetaSVM	Benign	-0.59	T
MutationAssessor	Benign	1.7	L;.;.
PrimateAI	Uncertain	0.61	T
PROVEAN	Uncertain	-2.5	D;D;D
REVEL	Uncertain	0.29
Sift	Benign	0.048	D;T;T
Sift4G	Benign	0.10	T;T;D
Polyphen		0.81	P;.;.
Vest4		0.19
MutPred		0.45		Loss of stability (P = 0.3484);.;.;
MVP		0.60
MPC		0.53
ClinPred		0.49	T
GERP RS		-8.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.32
gMVP		0.84

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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

Other links and lift over

dbSNP: rs151335200; hg19: chrX-152960007;