rs12391221

Positions:

• chrX-116444821-C-A

Variant summary

Our verdict is Likely benign. Variant got -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

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 Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC6A14	NM_007231.5	c.657-97C>A		intron_variant		ENST00000598581.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC6A14	ENST00000598581.3	c.657-97C>A		intron_variant		1	NM_007231.5	P1

Frequencies

GnomAD3 genomes AF: 0.694 AC: 76284 AN: 109991 Hom.: 18810 Cov.: 23 AF XY: 0.697 AC XY: 22539 AN XY: 32347

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

Gnomad4 AFR exome AF: 0.656

Gnomad4 AMR exome AF: 0.669

Gnomad4 ASJ exome AF: 0.790

Gnomad4 EAS exome AF: 0.952

Gnomad4 SAS exome AF: 0.757

Gnomad4 FIN exome AF: 0.764

Gnomad4 NFE exome AF: 0.684

Gnomad4 OTH exome AF: 0.714

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

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.809

Gnomad4 EAS AF: 0.953

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.701

Alfa AF: 0.687 Hom.: 26042

Bravo AF: 0.689

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12391221; hg19: -;