X-116436924-A-T

Position:

• chrX-116436924-A-T

Variant summary

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

The NM_007231.5(SLC6A14):​c.48+167A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 111,030 control chromosomes in the GnomAD database, including 1,772 homozygotes. There are 6,411 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 0.20 (1772 hom., 6411 hem., cov: 22)
• Consequence: SLC6A14 NM_007231.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.771

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC6A14	NM_007231.5	c.48+167A>T		intron_variant		ENST00000598581.3	NP_009162.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC6A14	ENST00000598581.3	c.48+167A>T		intron_variant		1	NM_007231.5	ENSP00000470801	P1

Frequencies

GnomAD3 genomes AF: 0.198 AC: 21999 AN: 110978 Hom.: 1771 Cov.: 22 AF XY: 0.192 AC XY: 6386 AN XY: 33220

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0380

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.198 AC: 22021 AN: 111030 Hom.: 1772 Cov.: 22 AF XY: 0.193 AC XY: 6411 AN XY: 33282

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.0381

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.197

Alfa AF: 0.217 Hom.: 1299

Bravo AF: 0.201

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.4
DANN	Benign	0.62

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: rs2312054; hg19: chrX-115568092;