X-116459133-C-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_007231.5(SLC6A14):​c.*178C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., 0 hem., cov: 21)
  • Exomes 𝑓: 0.000040 (0 hom. 5 hem.)
  • Failed GnomAD Quality Control
• Consequence: SLC6A14 NM_007231.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 16 publications found

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]

SLC6A14 Gene-Disease associations (from GenCC):

• cystic fibrosis

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS2: High Hemizygotes in GnomAdExome4 at 5 AR gene

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 108829 Hom.: 0 Cov.: 21

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: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000397 AC: 10 AN: 251614 Hom.: 0 Cov.: 4 AF XY: 0.0000704 AC XY: 5 AN XY: 71020

African (AFR) AF: 0.00 AC: 0 AN: 6757

American (AMR) AF: 0.00 AC: 0 AN: 8192

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 7993

East Asian (EAS) AF: 0.000531 AC: 10 AN: 18818

South Asian (SAS) AF: 0.00 AC: 0 AN: 9749

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 24673

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1111

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 158532

Other (OTH) AF: 0.00 AC: 0 AN: 15789

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 108829 Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0 AN XY: 31247

African (AFR) AF: 0.00 AC: 0 AN: 30070

American (AMR) AF: 0.00 AC: 0 AN: 10030

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2626

East Asian (EAS) AF: 0.00 AC: 0 AN: 3427

South Asian (SAS) AF: 0.00 AC: 0 AN: 2546

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5560

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 231

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 52202

Other (OTH) AF: 0.00 AC: 0 AN: 1467

Alfa AF: 0.00 Hom.: 3786

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.89
DANN	Benign	0.34
PhyloP100		0.23

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: rs2011162; hg19: chrX-115590299;