2-219209988-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005689.4(ABCB6):c.2479G>A(p.Gly827Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000028 in 1,461,872 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005689.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCB6 | NM_005689.4 | c.2479G>A | p.Gly827Arg | missense_variant | 19/19 | ENST00000265316.9 | |
ABCB6 | NM_001349828.2 | c.2341G>A | p.Gly781Arg | missense_variant | 18/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCB6 | ENST00000265316.9 | c.2479G>A | p.Gly827Arg | missense_variant | 19/19 | 1 | NM_005689.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.0000280 AC: 41AN: 1461872Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 727234
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2021 | The c.2479G>A (p.G827R) alteration is located in exon 19 (coding exon 19) of the ABCB6 gene. This alteration results from a G to A substitution at nucleotide position 2479, causing the glycine (G) at amino acid position 827 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at