rs2011162
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
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
NM_007231.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.231
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BS2
?
High Hemizygotes in GnomAdExome4 at 5 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A14 | NM_007231.5 | c.*178C>A | 3_prime_UTR_variant | 14/14 | ENST00000598581.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A14 | ENST00000598581.3 | c.*178C>A | 3_prime_UTR_variant | 14/14 | 1 | NM_007231.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 108829Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 31247 FAILED QC
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GnomAD4 exome AF: 0.0000397 AC: 10AN: 251614Hom.: 0 Cov.: 4 AF XY: 0.0000704 AC XY: 5AN XY: 71020
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GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 108829Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 31247
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at