rs16943320
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003486.7(SLC7A5):c.1141-126T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 890,950 control chromosomes in the GnomAD database, including 34,562 homozygotes. 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 0.26 ( 5520 hom., cov: 32)
Exomes 𝑓: 0.28 ( 29042 hom. )
Consequence
SLC7A5
NM_003486.7 intron
NM_003486.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.549
Genes affected
SLC7A5 (HGNC:11063): (solute carrier family 7 member 5) Enables L-leucine transmembrane transporter activity; L-tryptophan transmembrane transporter activity; and thyroid hormone transmembrane transporter activity. Involved in carboxylic acid transport; thyroid hormone transport; and xenobiotic transport. Located in cytosol; intracellular membrane-bounded organelle; and plasma membrane. Is integral component of membrane. Part of amino acid transport complex; apical plasma membrane; and microvillus membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC7A5 | NM_003486.7 | c.1141-126T>C | intron_variant | ENST00000261622.5 | |||
LOC124903753 | XR_007065175.1 | n.509A>G | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC7A5 | ENST00000261622.5 | c.1141-126T>C | intron_variant | 1 | NM_003486.7 | P1 | |||
SLC7A5 | ENST00000565644.5 | c.343-126T>C | intron_variant | 1 | |||||
ENST00000563687.1 | n.242A>G | non_coding_transcript_exon_variant | 1/2 | 3 | |||||
SLC7A5 | ENST00000563489.1 | n.33T>C | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.263 AC: 39820AN: 151188Hom.: 5502 Cov.: 32
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GnomAD4 exome AF: 0.284 AC: 210035AN: 739640Hom.: 29042 Cov.: 11 AF XY: 0.291 AC XY: 113094AN XY: 389236
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GnomAD4 genome ? AF: 0.264 AC: 39872AN: 151310Hom.: 5520 Cov.: 32 AF XY: 0.264 AC XY: 19502AN XY: 73940
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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