chr16-31483196-T-C
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_003041.4(SLC5A2):āc.60T>Cā(p.Ile20=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00116 in 1,614,016 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.0064 ( 17 hom., cov: 32)
Exomes š: 0.00061 ( 7 hom. )
Consequence
SLC5A2
NM_003041.4 synonymous
NM_003041.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0310
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 Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
Variant 16-31483196-T-C is Benign according to our data. Variant chr16-31483196-T-C is described in ClinVar as [Benign]. Clinvar id is 777013.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.031 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0064 (974/152232) while in subpopulation AFR AF= 0.0225 (934/41540). AF 95% confidence interval is 0.0213. There are 17 homozygotes in gnomad4. There are 439 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 17 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC5A2 | NM_003041.4 | c.60T>C | p.Ile20= | synonymous_variant | 1/14 | ENST00000330498.4 | |
SLC5A2 | XM_006721072.5 | c.60T>C | p.Ile20= | synonymous_variant | 1/13 | ||
SLC5A2 | XM_024450402.2 | c.60T>C | p.Ile20= | synonymous_variant | 1/11 | ||
SLC5A2 | NR_130783.2 | n.74T>C | non_coding_transcript_exon_variant | 1/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC5A2 | ENST00000330498.4 | c.60T>C | p.Ile20= | synonymous_variant | 1/14 | 1 | NM_003041.4 | P1 | |
SLC5A2 | ENST00000419665.6 | c.60T>C | p.Ile20= | synonymous_variant, NMD_transcript_variant | 1/12 | 1 | |||
SLC5A2 | ENST00000569576.5 | c.-4+128T>C | intron_variant | 4 | |||||
SLC5A2 | ENST00000562006.1 | n.59T>C | non_coding_transcript_exon_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00640 AC: 973AN: 152114Hom.: 17 Cov.: 32
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GnomAD3 exomes AF: 0.00168 AC: 423AN: 251380Hom.: 5 AF XY: 0.00110 AC XY: 149AN XY: 135908
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GnomAD4 exome AF: 0.000610 AC: 891AN: 1461784Hom.: 7 Cov.: 32 AF XY: 0.000481 AC XY: 350AN XY: 727182
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GnomAD4 genome AF: 0.00640 AC: 974AN: 152232Hom.: 17 Cov.: 32 AF XY: 0.00590 AC XY: 439AN XY: 74418
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Familial renal glucosuria Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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Name
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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