chrX-153688569-GA-G

Variant names:

• chrX-153688569-GA-G
• rs1557043702
• NM_005629.4:c.-5delA

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_005629.4(SLC6A8):​c.-5delA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 18)
  • Exomes 𝑓: 0.0000011 (0 hom. 0 hem.)
• Consequence: SLC6A8 NM_005629.4 5_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.25
• 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]

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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP6: Variant X-153688569-GA-G is Benign according to our data. Variant chrX-153688569-GA-G is described in ClinVar as Likely_benign. ClinVar VariationId is 516246.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005629.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC6A8	NM_005629.4	MANE Select	c.-5delA		5_prime_UTR	Exon 1 of 13	NP_005620.1	P48029-1
	SLC6A8	NM_001142805.2		c.-5delA		5_prime_UTR	Exon 1 of 13	NP_001136277.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC6A8	ENST00000253122.10	TSL:1 MANE Select	c.-5delA		5_prime_UTR	Exon 1 of 13	ENSP00000253122.5	P48029-1
	SLC6A8	ENST00000955775.1		c.-5delA		5_prime_UTR	Exon 1 of 13	ENSP00000625834.1
	SLC6A8	ENST00000922630.1		c.-5delA		5_prime_UTR	Exon 1 of 13	ENSP00000592689.1

Frequencies

GnomAD3 genomes Cov.: 18

GnomAD2 exomes AF: 0.00 AC: 0 AN: 45596 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000111 AC: 1 AN: 899351 Hom.: 0 Cov.: 17 AF XY: 0.00 AC XY: 0 AN XY: 277489

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 18077

American (AMR) AF: 0.00 AC: 0 AN: 14859

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13803

East Asian (EAS) AF: 0.00 AC: 0 AN: 16517

South Asian (SAS) AF: 0.00 AC: 0 AN: 37604

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28214

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2263

European-Non Finnish (NFE) AF: 0.00000136 AC: 1 AN: 732613

Other (OTH) AF: 0.00 AC: 0 AN: 35401

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 18

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.3

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

Other links and lift over

dbSNP: rs1557043702; hg19: chrX-152954024;