X-116459133-C-G

Variant names:

• chrX-116459133-C-G
• rs2011162
• NM_007231.5:c.*178C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007231.5(SLC6A14):​c.*178C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 360,017 control chromosomes in the GnomAD database, including 39,818 homozygotes. There are 57,455 hemizygotes 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 0.50 (10585 hom., 15426 hem., cov: 21)
  • Exomes 𝑓: 0.57 (29233 hom. 42029 hem.)
• Consequence: SLC6A14 NM_007231.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231

Genes affected

SLC6A14 (HGNC:11047): (solute carrier family 6 member 14) This gene encodes a member of the solute carrier family 6. Members of this family are sodium and chloride dependent neurotransmitter transporters. The encoded protein transports both neutral and cationic amino acids. This protein may also function as a beta-alanine carrier. Mutations in this gene may be associated with X-linked obesity. A pseudogene of this gene is found on chromosome X.[provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC6A14	NM_007231.5	c.*178C>G		3_prime_UTR_variant	Exon 14 of 14	ENST00000598581.3	NP_009162.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC6A14	ENST00000598581.3	c.*178C>G		3_prime_UTR_variant	Exon 14 of 14	1	NM_007231.5	ENSP00000470801.1
SLC6A14	ENST00000463626.1	n.*191C>G		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.496 AC: 53879 AN: 108736 Hom.: 10592 Cov.: 21 AF XY: 0.494 AC XY: 15406 AN XY: 31212

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.524

GnomAD4 exome AF: 0.571 AC: 143522 AN: 251235 Hom.: 29233 Cov.: 4 AF XY: 0.592 AC XY: 42029 AN XY: 70969

Gnomad4 AFR exome AF: 0.262

Gnomad4 AMR exome AF: 0.733

Gnomad4 ASJ exome AF: 0.655

Gnomad4 EAS exome AF: 0.465

Gnomad4 SAS exome AF: 0.434

Gnomad4 FIN exome AF: 0.560

Gnomad4 NFE exome AF: 0.595

Gnomad4 OTH exome AF: 0.563

GnomAD4 genome AF: 0.495 AC: 53893 AN: 108782 Hom.: 10585 Cov.: 21 AF XY: 0.493 AC XY: 15426 AN XY: 31268

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.524

Alfa AF: 0.528 Hom.: 3786

Bravo AF: 0.501

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.96
DANN	Benign	0.43

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

LitVar

Other links and lift over

dbSNP: rs2011162; hg19: chrX-115590299;