9-137008510-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001606.5(ABCA2):c.7181G>A(p.Arg2394Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00118 in 1,586,100 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001606.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCA2 | NM_001606.5 | c.7181G>A | p.Arg2394Gln | missense_variant | Exon 48 of 49 | ENST00000341511.11 | NP_001597.2 | |
ABCA2 | NM_212533.3 | c.7271G>A | p.Arg2424Gln | missense_variant | Exon 48 of 49 | NP_997698.1 | ||
ABCA2 | NM_001411042.1 | c.7178G>A | p.Arg2393Gln | missense_variant | Exon 47 of 48 | NP_001397971.1 | ||
ABCA2 | XM_047422921.1 | c.7268G>A | p.Arg2423Gln | missense_variant | Exon 47 of 48 | XP_047278877.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000736 AC: 112AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000609 AC: 123AN: 202012Hom.: 0 AF XY: 0.000621 AC XY: 68AN XY: 109544
GnomAD4 exome AF: 0.00123 AC: 1766AN: 1433768Hom.: 3 Cov.: 42 AF XY: 0.00120 AC XY: 856AN XY: 710598
GnomAD4 genome AF: 0.000735 AC: 112AN: 152332Hom.: 0 Cov.: 32 AF XY: 0.000631 AC XY: 47AN XY: 74482
ClinVar
Submissions by phenotype
not provided Uncertain:2
In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 2424 of the ABCA2 protein (p.Arg2424Gln). This variant is present in population databases (rs55971316, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with ABCA2-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
not specified Uncertain:1
The c.7271G>A (p.R2424Q) alteration is located in exon 48 (coding exon 48) of the ABCA2 gene. This alteration results from a G to A substitution at nucleotide position 7271, causing the arginine (R) at amino acid position 2424 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