rs56993779
Positions:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP6_ModerateBP7BA1
The NM_138817.3(SLC7A13):c.1413_*7del variant causes a stop retained, 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 1,572,080 control chromosomes in the GnomAD database, including 20,645 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.13 ( 1705 hom., cov: 30)
Exomes 𝑓: 0.15 ( 18940 hom. )
Consequence
SLC7A13
NM_138817.3 stop_retained, 3_prime_UTR
NM_138817.3 stop_retained, 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.83
Genes affected
SLC7A13 (HGNC:23092): (solute carrier family 7 member 13) Predicted to enable L-amino acid transmembrane transporter activity. Predicted to be involved in L-cystine transport; L-glutamate transmembrane transport; and aspartate transmembrane transport. Predicted to be integral component of membrane. Predicted to be active in apical plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP6
?
Variant 8-86214405-TCCGACATC-T is Benign according to our data. Variant chr8-86214405-TCCGACATC-T is described in ClinVar as [Benign]. Clinvar id is 1620765.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=2.83 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC7A13 | NM_138817.3 | c.1413_*7del | stop_retained_variant, 3_prime_UTR_variant | 4/4 | ENST00000297524.8 | ||
SLC7A13 | XM_011516867.3 | c.1386_*7del | stop_retained_variant, 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC7A13 | ENST00000297524.8 | c.1413_*7del | stop_retained_variant, 3_prime_UTR_variant | 4/4 | 1 | NM_138817.3 | P1 | ||
SLC7A13 | ENST00000419776.2 | c.*212_*219del | 3_prime_UTR_variant | 5/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.129 AC: 19557AN: 151998Hom.: 1700 Cov.: 30
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GnomAD3 exomes AF: 0.181 AC: 42497AN: 234406Hom.: 4632 AF XY: 0.187 AC XY: 23905AN XY: 127872
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GnomAD4 exome AF: 0.150 AC: 212309AN: 1419964Hom.: 18940 AF XY: 0.155 AC XY: 109814AN XY: 707404
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GnomAD4 genome ? AF: 0.129 AC: 19574AN: 152116Hom.: 1705 Cov.: 30 AF XY: 0.132 AC XY: 9837AN XY: 74348
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at