chr12-21300490-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001386879.1(SLCO1A2):c.768C>T(p.Asn256=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00238 in 1,613,398 control chromosomes in the GnomAD database, including 86 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.013 ( 46 hom., cov: 32)
Exomes 𝑓: 0.0013 ( 40 hom. )
Consequence
SLCO1A2
NM_001386879.1 synonymous
NM_001386879.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.22
Genes affected
SLCO1A2 (HGNC:10956): (solute carrier organic anion transporter family member 1A2) This gene encodes a sodium-independent transporter which mediates cellular uptake of organic ions in the liver. Its substrates include bile acids, bromosulphophthalein, and some steroidal compounds. The protein is a member of the SLC21A family of solute carriers. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2008]
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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=-0.48).
BP6
?
Variant 12-21300490-G-A is Benign according to our data. Variant chr12-21300490-G-A is described in ClinVar as [Benign]. Clinvar id is 788577.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.22 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0128 (1945/152120) while in subpopulation AFR AF= 0.0442 (1834/41490). AF 95% confidence interval is 0.0425. There are 46 homozygotes in gnomad4. There are 947 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 45 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLCO1A2 | NM_001386879.1 | c.768C>T | p.Asn256= | synonymous_variant | 8/15 | ENST00000683939.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO1A2 | ENST00000683939.1 | c.768C>T | p.Asn256= | synonymous_variant | 8/15 | NM_001386879.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0127 AC: 1932AN: 152002Hom.: 45 Cov.: 32
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GnomAD3 exomes AF: 0.00337 AC: 845AN: 250416Hom.: 13 AF XY: 0.00251 AC XY: 340AN XY: 135310
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GnomAD4 exome AF: 0.00129 AC: 1891AN: 1461278Hom.: 40 Cov.: 31 AF XY: 0.00110 AC XY: 800AN XY: 726918
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GnomAD4 genome ? AF: 0.0128 AC: 1945AN: 152120Hom.: 46 Cov.: 32 AF XY: 0.0127 AC XY: 947AN XY: 74356
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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 | Jul 13, 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