10-99844450-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_000392.5(ABCC2):c.3972C>T(p.Ile1324Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 1,613,504 control chromosomes in the GnomAD database, including 105,110 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000392.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCC2 | NM_000392.5 | c.3972C>T | p.Ile1324Ile | synonymous_variant | Exon 28 of 32 | ENST00000647814.1 | NP_000383.2 | |
ABCC2 | XM_006717630.4 | c.3276C>T | p.Ile1092Ile | synonymous_variant | Exon 23 of 27 | XP_006717693.1 | ||
ABCC2 | XR_945604.4 | n.4177C>T | non_coding_transcript_exon_variant | Exon 28 of 30 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.327 AC: 49678AN: 152002Hom.: 8473 Cov.: 33
GnomAD3 exomes AF: 0.341 AC: 85500AN: 250980Hom.: 14799 AF XY: 0.343 AC XY: 46531AN XY: 135696
GnomAD4 exome AF: 0.361 AC: 528097AN: 1461384Hom.: 96644 Cov.: 51 AF XY: 0.361 AC XY: 262439AN XY: 727046
GnomAD4 genome AF: 0.327 AC: 49695AN: 152120Hom.: 8466 Cov.: 33 AF XY: 0.326 AC XY: 24231AN XY: 74362
ClinVar
Submissions by phenotype
not provided Benign:3
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This variant is associated with the following publications: (PMID: 17997497, 24743544, 21541183, 25087612) -
Dubin-Johnson syndrome Benign:2
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not specified Benign:1
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ABCC2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at