22-41249749-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_002883.4(RANGAP1):c.1552G>A(p.Val518Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 1,461,542 control chromosomes in the GnomAD database, with no homozygous occurrence. 13/21 in silico tools predict 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
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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 |
---|---|---|---|---|---|---|---|---|
RANGAP1 | NM_002883.4 | c.1552G>A | p.Val518Met | missense_variant | Exon 14 of 16 | ENST00000356244.8 | NP_002874.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RANGAP1 | ENST00000356244.8 | c.1552G>A | p.Val518Met | missense_variant | Exon 14 of 16 | 1 | NM_002883.4 | ENSP00000348577.3 | ||
RANGAP1 | ENST00000405486.5 | c.1552G>A | p.Val518Met | missense_variant | Exon 15 of 17 | 1 | ENSP00000385866.1 | |||
RANGAP1 | ENST00000455915.6 | c.1552G>A | p.Val518Met | missense_variant | Exon 13 of 15 | 1 | ENSP00000401470.2 | |||
RANGAP1 | ENST00000705116.1 | c.1552G>A | p.Val518Met | missense_variant | Exon 14 of 16 | ENSP00000516069.1 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251366Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135878
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461542Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727112
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1552G>A (p.V518M) alteration is located in exon 14 (coding exon 13) of the RANGAP1 gene. This alteration results from a G to A substitution at nucleotide position 1552, causing the valine (V) at amino acid position 518 to be replaced by a methionine (M). 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