chr20-4869923-G-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_005116.6(SLC23A2):c.1233C>A(p.Pro411=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000384 in 1,326,462 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 (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000042 ( 0 hom. )
Consequence
SLC23A2
NM_005116.6 synonymous
NM_005116.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.143
Genes affected
SLC23A2 (HGNC:10973): (solute carrier family 23 member 2) The absorption of vitamin C into the body and its distribution to organs requires two sodium-dependent vitamin C transporters. This gene encodes one of the two required transporters and the encoded protein accounts for tissue-specific uptake of vitamin C. Previously, this gene had an official symbol of SLC23A1. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
Variant 20-4869923-G-T is Benign according to our data. Variant chr20-4869923-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 750086.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.143 with no splicing effect.
BS2
High AC in GnomAdExome4 at 49 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC23A2 | NM_005116.6 | c.1233C>A | p.Pro411= | synonymous_variant | 12/17 | ENST00000338244.6 | |
SLC23A2 | NM_203327.2 | c.1233C>A | p.Pro411= | synonymous_variant | 12/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC23A2 | ENST00000338244.6 | c.1233C>A | p.Pro411= | synonymous_variant | 12/17 | 1 | NM_005116.6 | P1 | |
SLC23A2 | ENST00000379333.5 | c.1233C>A | p.Pro411= | synonymous_variant | 12/17 | 1 | P1 | ||
SLC23A2 | ENST00000468355.5 | n.1599C>A | non_coding_transcript_exon_variant | 12/12 | 1 | ||||
SLC23A2 | ENST00000423430.1 | c.504C>A | p.Pro168= | synonymous_variant | 4/8 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000133 AC: 2AN: 150810Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000779 AC: 15AN: 192512Hom.: 0 AF XY: 0.0000860 AC XY: 9AN XY: 104680
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GnomAD4 exome AF: 0.0000417 AC: 49AN: 1175652Hom.: 0 Cov.: 32 AF XY: 0.0000443 AC XY: 26AN XY: 586254
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GnomAD4 genome AF: 0.0000133 AC: 2AN: 150810Hom.: 0 Cov.: 31 AF XY: 0.0000136 AC XY: 1AN XY: 73546
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 23, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at