chr16-31484655-C-G
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6
The NM_003041.4(SLC5A2):c.127-18C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0001 in 1,604,478 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000099 ( 0 hom. )
Consequence
SLC5A2
NM_003041.4 intron
NM_003041.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.424
Genes affected
SLC5A2 (HGNC:11037): (solute carrier family 5 member 2) This gene encodes a member of the sodium glucose cotransporter family which are sodium-dependent glucose transport proteins. The encoded protein is the major cotransporter involved in glucose reabsorption in the kidney. Mutations in this gene are associated with renal glucosuria. Two transcript variants, one protein-coding and one not, have been found for this gene. [provided by RefSeq, Feb 2015]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
BP6
Variant 16-31484655-C-G is Benign according to our data. Variant chr16-31484655-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 3047822.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC5A2 | NM_003041.4 | c.127-18C>G | intron_variant | ENST00000330498.4 | |||
SLC5A2 | XM_006721072.5 | c.127-18C>G | intron_variant | ||||
SLC5A2 | XM_024450402.2 | c.127-18C>G | intron_variant | ||||
SLC5A2 | NR_130783.2 | n.141-18C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC5A2 | ENST00000330498.4 | c.127-18C>G | intron_variant | 1 | NM_003041.4 | P1 | |||
SLC5A2 | ENST00000419665.6 | c.127-18C>G | intron_variant, NMD_transcript_variant | 1 | |||||
SLC5A2 | ENST00000569576.5 | c.-3-18C>G | intron_variant | 4 | |||||
SLC5A2 | ENST00000562006.1 | n.126-18C>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152144Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000135 AC: 33AN: 244354Hom.: 0 AF XY: 0.000166 AC XY: 22AN XY: 132646
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GnomAD4 exome AF: 0.0000992 AC: 144AN: 1452334Hom.: 0 Cov.: 32 AF XY: 0.000102 AC XY: 74AN XY: 722874
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GnomAD4 genome AF: 0.000112 AC: 17AN: 152144Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74330
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
SLC5A2-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 25, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AL_spliceai
Position offset: 18
Find out detailed SpliceAI scores and Pangolin per-transcript scores at