chr11-64562055-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_018484.4(SLC22A11):c.549G>A(p.Ala183=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000269 in 1,613,700 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0015 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00014 ( 0 hom. )
Consequence
SLC22A11
NM_018484.4 synonymous
NM_018484.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.07
Genes affected
SLC22A11 (HGNC:18120): (solute carrier family 22 member 11) The protein encoded by this gene is involved in the sodium-independent transport and excretion of organic anions, some of which are potentially toxic. The encoded protein is an integral membrane protein and is found mainly in the kidney and in the placenta, where it may act to prevent potentially harmful organic anions from reaching the fetus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
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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=-0.87).
BP6
?
Variant 11-64562055-G-A is Benign according to our data. Variant chr11-64562055-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3053321.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.08 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC22A11 | NM_018484.4 | c.549G>A | p.Ala183= | synonymous_variant | 3/10 | ENST00000301891.9 | |
SLC22A11 | NM_001307985.2 | c.549G>A | p.Ala183= | synonymous_variant | 3/8 | ||
SLC22A11 | XM_011545167.2 | c.150G>A | p.Ala50= | synonymous_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC22A11 | ENST00000301891.9 | c.549G>A | p.Ala183= | synonymous_variant | 3/10 | 1 | NM_018484.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00152 AC: 232AN: 152176Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.000407 AC: 102AN: 250732Hom.: 0 AF XY: 0.000287 AC XY: 39AN XY: 135730
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GnomAD4 exome AF: 0.000137 AC: 200AN: 1461406Hom.: 0 Cov.: 31 AF XY: 0.000111 AC XY: 81AN XY: 727008
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GnomAD4 genome ? AF: 0.00154 AC: 234AN: 152294Hom.: 2 Cov.: 32 AF XY: 0.00146 AC XY: 109AN XY: 74470
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SLC22A11-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 23, 2022 | 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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BayesDel_noAF
Benign
Cadd
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Dann
Benign
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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