22-41254388-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_002883.4(RANGAP1):c.1180G>A(p.Glu394Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,764 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002883.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RANGAP1 | NM_002883.4 | c.1180G>A | p.Glu394Lys | missense_variant | Exon 11 of 16 | ENST00000356244.8 | NP_002874.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RANGAP1 | ENST00000356244.8 | c.1180G>A | p.Glu394Lys | missense_variant | Exon 11 of 16 | 1 | NM_002883.4 | ENSP00000348577.3 | ||
RANGAP1 | ENST00000405486.5 | c.1180G>A | p.Glu394Lys | missense_variant | Exon 12 of 17 | 1 | ENSP00000385866.1 | |||
RANGAP1 | ENST00000455915.6 | c.1180G>A | p.Glu394Lys | missense_variant | Exon 10 of 15 | 1 | ENSP00000401470.2 | |||
RANGAP1 | ENST00000705116.1 | c.1180G>A | p.Glu394Lys | missense_variant | Exon 11 of 16 | ENSP00000516069.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152126Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000804 AC: 2AN: 248910Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134774
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461638Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727122
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152126Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1180G>A (p.E394K) alteration is located in exon 11 (coding exon 10) of the RANGAP1 gene. This alteration results from a G to A substitution at nucleotide position 1180, causing the glutamic acid (E) at amino acid position 394 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