16-87838708-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003486.7(SLC7A5):c.1043+6C>T variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00334 in 1,609,204 control chromosomes in the GnomAD database, including 120 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.018 ( 65 hom., cov: 32)
Exomes 𝑓: 0.0018 ( 55 hom. )
Consequence
SLC7A5
NM_003486.7 splice_donor_region, intron
NM_003486.7 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.00001699
2
Clinical Significance
Conservation
PhyloP100: -1.58
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 16-87838708-G-A is Benign according to our data. Variant chr16-87838708-G-A is described in ClinVar as [Benign]. Clinvar id is 781231.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0597 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC7A5 | NM_003486.7 | c.1043+6C>T | splice_donor_region_variant, intron_variant | ENST00000261622.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC7A5 | ENST00000261622.5 | c.1043+6C>T | splice_donor_region_variant, intron_variant | 1 | NM_003486.7 | P1 | |||
SLC7A5 | ENST00000565644.5 | c.245+6C>T | splice_donor_region_variant, intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0178 AC: 2712AN: 152226Hom.: 65 Cov.: 32
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GnomAD3 exomes AF: 0.00463 AC: 1163AN: 251050Hom.: 21 AF XY: 0.00324 AC XY: 440AN XY: 135794
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GnomAD4 exome AF: 0.00183 AC: 2663AN: 1456860Hom.: 55 Cov.: 30 AF XY: 0.00154 AC XY: 1118AN XY: 725112
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GnomAD4 genome AF: 0.0178 AC: 2716AN: 152344Hom.: 65 Cov.: 32 AF XY: 0.0174 AC XY: 1295AN XY: 74484
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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 | Dec 11, 2017 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at