rs2071877

Positions:

• chrX-116457272-C-T

Variant summary

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

The NM_007231.5(SLC6A14):​c.1615-337C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 110,045 control chromosomes in the GnomAD database, including 6,397 homozygotes. There are 12,343 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 0.38 (6397 hom., 12343 hem., cov: 23)
• Consequence: SLC6A14 NM_007231.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC6A14	NM_007231.5	c.1615-337C>T		intron_variant		ENST00000598581.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC6A14	ENST00000598581.3	c.1615-337C>T		intron_variant		1	NM_007231.5	P1
SLC6A14	ENST00000463626.1	n.211-1537C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.383 AC: 42123 AN: 109991 Hom.: 6404 Cov.: 23 AF XY: 0.380 AC XY: 12319 AN XY: 32429

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.352

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.356

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.383 AC: 42144 AN: 110045 Hom.: 6397 Cov.: 23 AF XY: 0.380 AC XY: 12343 AN XY: 32493

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.354

Alfa AF: 0.357 Hom.: 2363

Bravo AF: 0.379

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2071877; hg19: chrX-115588438;