6-13634458-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_005493.3(RANBP9):c.1768G>A(p.Glu590Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000353 in 1,613,474 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005493.3 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 |
---|---|---|---|---|---|---|---|---|
RANBP9 | NM_005493.3 | c.1768G>A | p.Glu590Lys | missense_variant | Exon 11 of 14 | ENST00000011619.6 | NP_005484.2 | |
RANBP9 | XM_017010149.2 | c.1102G>A | p.Glu368Lys | missense_variant | Exon 11 of 14 | XP_016865638.1 | ||
RANBP9 | XM_047418032.1 | c.1081G>A | p.Glu361Lys | missense_variant | Exon 11 of 14 | XP_047273988.1 | ||
RANBP9 | XM_011514205.3 | c.1526-1937G>A | intron_variant | Intron 9 of 11 | XP_011512507.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251044Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135656
GnomAD4 exome AF: 0.0000287 AC: 42AN: 1461208Hom.: 0 Cov.: 30 AF XY: 0.0000316 AC XY: 23AN XY: 726880
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74446
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1768G>A (p.E590K) alteration is located in exon 11 (coding exon 11) of the RANBP9 gene. This alteration results from a G to A substitution at nucleotide position 1768, causing the glutamic acid (E) at amino acid position 590 to be replaced by a lysine (K). 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