chr5-128186851-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001046.3(SLC12A2):c.*220C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 401,780 control chromosomes in the GnomAD database, including 10,394 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.21 ( 3590 hom., cov: 32)
Exomes 𝑓: 0.23 ( 6804 hom. )
Consequence
SLC12A2
NM_001046.3 3_prime_UTR
NM_001046.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.257
Genes affected
SLC12A2 (HGNC:10911): (solute carrier family 12 member 2) The protein encoded by this gene mediates sodium and chloride transport and reabsorption. The encoded protein is a membrane protein and is important in maintaining proper ionic balance and cell volume. This protein is phosphorylated in response to DNA damage. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
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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=-0.82).
BP6
Variant 5-128186851-C-T is Benign according to our data. Variant chr5-128186851-C-T is described in ClinVar as [Benign]. Clinvar id is 1294739.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC12A2 | NM_001046.3 | c.*220C>T | 3_prime_UTR_variant | 27/27 | ENST00000262461.7 | ||
SLC12A2 | NM_001256461.2 | c.*220C>T | 3_prime_UTR_variant | 26/26 | |||
SLC12A2 | NR_046207.2 | n.4114C>T | non_coding_transcript_exon_variant | 27/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC12A2 | ENST00000262461.7 | c.*220C>T | 3_prime_UTR_variant | 27/27 | 1 | NM_001046.3 | P4 | ||
SLC12A2 | ENST00000343225.4 | c.*220C>T | 3_prime_UTR_variant | 26/26 | 1 | A2 | |||
SLC12A2 | ENST00000509205.5 | c.*472C>T | 3_prime_UTR_variant, NMD_transcript_variant | 27/27 | 1 |
Frequencies
GnomAD3 genomes AF: 0.212 AC: 32264AN: 151990Hom.: 3581 Cov.: 32
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GnomAD4 exome AF: 0.228 AC: 57039AN: 249672Hom.: 6804 Cov.: 4 AF XY: 0.227 AC XY: 29124AN XY: 128248
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GnomAD4 genome AF: 0.212 AC: 32292AN: 152108Hom.: 3590 Cov.: 32 AF XY: 0.216 AC XY: 16030AN XY: 74362
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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 | GeneDx | Nov 12, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at