chr2-219217783-G-A
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_005689.4(ABCB6):c.574C>T(p.Arg192Trp) variant causes a missense change. The variant allele was found at a frequency of 0.00183 in 1,613,266 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R192Q) has been classified as Likely benign.
Frequency
Consequence
NM_005689.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCB6 | NM_005689.4 | c.574C>T | p.Arg192Trp | missense_variant | 2/19 | ENST00000265316.9 | |
ABCB6 | NM_001349828.2 | c.549+342C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCB6 | ENST00000265316.9 | c.574C>T | p.Arg192Trp | missense_variant | 2/19 | 1 | NM_005689.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00158 AC: 240AN: 151962Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.00157 AC: 392AN: 249650Hom.: 0 AF XY: 0.00153 AC XY: 206AN XY: 135066
GnomAD4 exome AF: 0.00186 AC: 2716AN: 1461190Hom.: 8 Cov.: 33 AF XY: 0.00190 AC XY: 1382AN XY: 726942
GnomAD4 genome AF: 0.00158 AC: 240AN: 152076Hom.: 1 Cov.: 31 AF XY: 0.00139 AC XY: 103AN XY: 74352
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | ABCB6: BS1, BS2 - |
Uncertain significance, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2024 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Acute intermittent porphyria Benign:1
Benign, criteria provided, single submitter | clinical testing | Phillips Lab, Hematology, University of Utah | Aug 16, 2021 | - - |
Variegate porphyria Benign:1
Benign, criteria provided, single submitter | clinical testing | Phillips Lab, Hematology, University of Utah | Aug 16, 2021 | - - |
Protoporphyria, erythropoietic, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Phillips Lab, Hematology, University of Utah | Aug 16, 2021 | - - |
Hereditary coproporphyria Benign:1
Benign, criteria provided, single submitter | clinical testing | Phillips Lab, Hematology, University of Utah | Aug 16, 2021 | - - |
Langereis blood group Other:1
Affects, no assertion criteria provided | literature only | OMIM | Feb 01, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at