17-60447705-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_006380.5(APPBP2):c.1634G>A(p.Arg545Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000967 in 1,613,972 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006380.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APPBP2 | NM_006380.5 | c.1634G>A | p.Arg545Gln | missense_variant | Exon 13 of 13 | ENST00000083182.8 | NP_006371.2 | |
APPBP2 | NM_001282476.2 | c.1421G>A | p.Arg474Gln | missense_variant | Exon 12 of 12 | NP_001269405.1 | ||
APPBP2 | XM_047435116.1 | c.1502G>A | p.Arg501Gln | missense_variant | Exon 13 of 13 | XP_047291072.1 | ||
APPBP2 | XM_047435118.1 | c.1376G>A | p.Arg459Gln | missense_variant | Exon 12 of 12 | XP_047291074.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000437 AC: 11AN: 251474Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135908
GnomAD4 exome AF: 0.000102 AC: 149AN: 1461836Hom.: 0 Cov.: 31 AF XY: 0.0000935 AC XY: 68AN XY: 727218
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1634G>A (p.R545Q) alteration is located in exon 13 (coding exon 13) of the APPBP2 gene. This alteration results from a G to A substitution at nucleotide position 1634, causing the arginine (R) at amino acid position 545 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