chr11-64556035-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_018484.4(SLC22A11):c.36C>T(p.Gly12=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00115 in 1,612,884 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0061 ( 12 hom., cov: 32)
Exomes 𝑓: 0.00064 ( 10 hom. )
Consequence
SLC22A11
NM_018484.4 synonymous
NM_018484.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.84
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
?
Variant 11-64556035-C-T is Benign according to our data. Variant chr11-64556035-C-T is described in ClinVar as [Benign]. Clinvar id is 711553.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.84 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00613 (934/152324) while in subpopulation AFR AF= 0.0206 (856/41562). AF 95% confidence interval is 0.0195. There are 12 homozygotes in gnomad4. There are 422 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 12 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC22A11 | NM_018484.4 | c.36C>T | p.Gly12= | synonymous_variant | 1/10 | ENST00000301891.9 | |
SLC22A11 | NM_001307985.2 | c.36C>T | p.Gly12= | synonymous_variant | 1/8 | ||
SLC22A11 | XM_011545167.2 | c.-260C>T | 5_prime_UTR_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC22A11 | ENST00000301891.9 | c.36C>T | p.Gly12= | synonymous_variant | 1/10 | 1 | NM_018484.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00614 AC: 934AN: 152206Hom.: 12 Cov.: 32
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GnomAD3 exomes AF: 0.00161 AC: 403AN: 250094Hom.: 5 AF XY: 0.00118 AC XY: 159AN XY: 135248
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GnomAD4 exome AF: 0.000635 AC: 928AN: 1460560Hom.: 10 Cov.: 31 AF XY: 0.000564 AC XY: 410AN XY: 726626
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GnomAD4 genome ? AF: 0.00613 AC: 934AN: 152324Hom.: 12 Cov.: 32 AF XY: 0.00567 AC XY: 422AN XY: 74480
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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 | Invitae | May 31, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
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