chr10-99818884-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP3BP4_StrongBP6
The NM_000392.5(ABCC2):c.2366C>T(p.Ser789Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000265 in 1,614,160 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. S789S) has been classified as Uncertain significance.
Frequency
Consequence
NM_000392.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCC2 | NM_000392.5 | c.2366C>T | p.Ser789Phe | missense_variant | 18/32 | ENST00000647814.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC2 | ENST00000647814.1 | c.2366C>T | p.Ser789Phe | missense_variant | 18/32 | NM_000392.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000269 AC: 41AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000629 AC: 158AN: 251278Hom.: 0 AF XY: 0.000581 AC XY: 79AN XY: 135860
GnomAD4 exome AF: 0.000265 AC: 387AN: 1461884Hom.: 1 Cov.: 32 AF XY: 0.000259 AC XY: 188AN XY: 727240
GnomAD4 genome AF: 0.000269 AC: 41AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74450
ClinVar
Submissions by phenotype
Dubin-Johnson syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
ABCC2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 01, 2019 | 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). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at