rs12391221

Variant names:

• chrX-116444821-C-A
• rs12391221
• NM_007231.5:c.657-97C>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_007231.5(SLC6A14):​c.657-97C>A variant causes a intron 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 0.69 (18809 hom., 22561 hem., cov: 23)
  • Exomes 𝑓: 0.70 (138334 hom. 156407 hem.)
  • Failed GnomAD Quality Control
• Consequence: SLC6A14 NM_007231.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 3 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=0.433).

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.657-97C>A		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.657-97C>A		intron	N/A	ENSP00000470801.1	Q9UN76
	SLC6A14	ENST00000961161.1		c.657-97C>A		intron	N/A	ENSP00000631220.1
	SLC6A14	ENST00000905559.1		c.525-97C>A		intron	N/A	ENSP00000575618.1

Frequencies

GnomAD3 genomes AF: 0.694 AC: 76284 AN: 109991 Hom.: 18810 Cov.: 23

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.903

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.701

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.704 AC: 548664 AN: 779476 Hom.: 138334 AF XY: 0.719 AC XY: 156407 AN XY: 217574

African (AFR) AF: 0.656 AC: 12780 AN: 19468

American (AMR) AF: 0.669 AC: 20752 AN: 30998

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 12888 AN: 16310

East Asian (EAS) AF: 0.952 AC: 26524 AN: 27853

South Asian (SAS) AF: 0.757 AC: 33486 AN: 44208

European-Finnish (FIN) AF: 0.764 AC: 29261 AN: 38276

Middle Eastern (MID) AF: 0.714 AC: 1782 AN: 2496

European-Non Finnish (NFE) AF: 0.684 AC: 386156 AN: 564794

Other (OTH) AF: 0.714 AC: 25035 AN: 35073

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.693 AC: 76300 AN: 110043 Hom.: 18809 Cov.: 23 AF XY: 0.696 AC XY: 22561 AN XY: 32407

African (AFR) AF: 0.655 AC: 19836 AN: 30279

American (AMR) AF: 0.664 AC: 6854 AN: 10325

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 2118 AN: 2618

East Asian (EAS) AF: 0.953 AC: 3309 AN: 3473

South Asian (SAS) AF: 0.752 AC: 1957 AN: 2604

European-Finnish (FIN) AF: 0.773 AC: 4466 AN: 5776

Middle Eastern (MID) AF: 0.729 AC: 156 AN: 214

European-Non Finnish (NFE) AF: 0.684 AC: 35940 AN: 52578

Other (OTH) AF: 0.701 AC: 1047 AN: 1493

Alfa AF: 0.686 Hom.: 37297

Bravo AF: 0.689

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.43
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs12391221;