2-219210026-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_005689.4(ABCB6):c.2441G>A(p.Arg814Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,614,138 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 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 -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCB6 | ENST00000265316.9 | c.2441G>A | p.Arg814Gln | missense_variant | Exon 19 of 19 | 1 | NM_005689.4 | ENSP00000265316.3 | ||
ENSG00000284820 | ENST00000446716.5 | n.*4225G>A | non_coding_transcript_exon_variant | Exon 22 of 22 | 2 | ENSP00000398528.1 | ||||
ENSG00000284820 | ENST00000446716.5 | n.*4225G>A | 3_prime_UTR_variant | Exon 22 of 22 | 2 | ENSP00000398528.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251482Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135916
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1461826Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20AN XY: 727218
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74476
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.2441G>A (p.R814Q) 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 2441, causing the arginine (R) at amino acid position 814 to be replaced by a glutamine (Q). 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