chr16-31484657-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_003041.4(SLC5A2):c.127-16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000038 in 1,604,904 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000041 ( 0 hom. )
Consequence
SLC5A2
NM_003041.4 intron
NM_003041.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.776
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 -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC5A2 | NM_003041.4 | c.127-16C>T | intron_variant | Intron 1 of 13 | ENST00000330498.4 | NP_003032.1 | ||
SLC5A2 | XM_006721072.5 | c.127-16C>T | intron_variant | Intron 1 of 12 | XP_006721135.3 | |||
SLC5A2 | XM_024450402.2 | c.127-16C>T | intron_variant | Intron 1 of 10 | XP_024306170.2 | |||
SLC5A2 | NR_130783.2 | n.141-16C>T | intron_variant | Intron 1 of 11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC5A2 | ENST00000330498.4 | c.127-16C>T | intron_variant | Intron 1 of 13 | 1 | NM_003041.4 | ENSP00000327943.3 | |||
SLC5A2 | ENST00000419665.6 | n.127-16C>T | intron_variant | Intron 1 of 11 | 1 | ENSP00000410601.2 | ||||
SLC5A2 | ENST00000569576.5 | c.-3-16C>T | intron_variant | Intron 1 of 4 | 4 | ENSP00000455143.1 | ||||
SLC5A2 | ENST00000562006.1 | n.126-16C>T | intron_variant | Intron 1 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152148Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000368 AC: 9AN: 244666Hom.: 0 AF XY: 0.0000301 AC XY: 4AN XY: 132758
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GnomAD4 exome AF: 0.0000406 AC: 59AN: 1452638Hom.: 0 Cov.: 32 AF XY: 0.0000470 AC XY: 34AN XY: 723016
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74454
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ClinVar
Not reported inComputational scores
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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