rs2271090
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001037984.3(SLC38A10):c.913-178T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,044 control chromosomes in the GnomAD database, including 22,584 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 0.51 ( 22584 hom., cov: 32)
Consequence
SLC38A10
NM_001037984.3 intron
NM_001037984.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.17
Genes affected
SLC38A10 (HGNC:28237): (solute carrier family 38 member 10) Predicted to enable amino acid transmembrane transporter activity. Predicted to be involved in amino acid transmembrane transport. Predicted to act upstream of or within bone development. Located in Golgi apparatus. [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=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC38A10 | NM_001037984.3 | c.913-178T>C | intron_variant | ENST00000374759.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC38A10 | ENST00000374759.8 | c.913-178T>C | intron_variant | 5 | NM_001037984.3 | A2 | |||
SLC38A10 | ENST00000288439.9 | c.913-178T>C | intron_variant | 1 | P2 | ||||
SLC38A10 | ENST00000542075.5 | n.1515-178T>C | intron_variant, non_coding_transcript_variant | 2 | |||||
SLC38A10 | ENST00000546352.1 | n.440-1781T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.513 AC: 77884AN: 151926Hom.: 22540 Cov.: 32
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.513 AC: 77983AN: 152044Hom.: 22584 Cov.: 32 AF XY: 0.504 AC XY: 37469AN XY: 74316
GnomAD4 genome
?
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37469
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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