rs2071877

Variant names:

• chrX-116457272-C-T
• rs2071877
• NM_007231.5:c.1615-337C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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 -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007231.5. 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
	SLC6A14	NM_007231.5	MANE Select	c.1615-337C>T		intron	N/A	NP_009162.1	Q9UN76

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC6A14	ENST00000598581.3	TSL:1 MANE Select	c.1615-337C>T		intron	N/A	ENSP00000470801.1	Q9UN76
	SLC6A14	ENST00000961161.1		c.1612-337C>T		intron	N/A	ENSP00000631220.1
	SLC6A14	ENST00000905559.1		c.1483-337C>T		intron	N/A	ENSP00000575618.1

Frequencies

GnomAD3 genomes AF: 0.383 AC: 42123 AN: 109991 Hom.: 6404 Cov.: 23

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

African (AFR) AF: 0.559 AC: 16969 AN: 30361

American (AMR) AF: 0.232 AC: 2407 AN: 10372

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 639 AN: 2617

East Asian (EAS) AF: 0.527 AC: 1824 AN: 3460

South Asian (SAS) AF: 0.518 AC: 1367 AN: 2640

European-Finnish (FIN) AF: 0.378 AC: 2176 AN: 5756

Middle Eastern (MID) AF: 0.364 AC: 75 AN: 206

European-Non Finnish (NFE) AF: 0.305 AC: 16011 AN: 52451

Other (OTH) AF: 0.354 AC: 535 AN: 1511

Alfa AF: 0.357 Hom.: 2363

Bravo AF: 0.379

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.74
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs2071877; hg19: chrX-115588438;