5-131429187-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016340.6(RAPGEF6):c.4495G>A(p.Asp1499Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000144 in 1,460,258 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016340.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAPGEF6 | NM_016340.6 | c.4495G>A | p.Asp1499Asn | missense_variant | Exon 27 of 28 | ENST00000509018.6 | NP_057424.3 | |
RAPGEF6 | NM_001164386.2 | c.4519G>A | p.Asp1507Asn | missense_variant | Exon 28 of 29 | NP_001157858.1 | ||
RAPGEF6 | NM_001164387.2 | c.4504+1672G>A | intron_variant | Intron 28 of 28 | NP_001157859.1 | |||
RAPGEF6 | NM_001164388.2 | c.4489+1672G>A | intron_variant | Intron 27 of 27 | NP_001157860.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAPGEF6 | ENST00000509018.6 | c.4495G>A | p.Asp1499Asn | missense_variant | Exon 27 of 28 | 1 | NM_016340.6 | ENSP00000421684.1 | ||
ENSG00000273217 | ENST00000514667.1 | c.4645G>A | p.Asp1549Asn | missense_variant | Exon 28 of 29 | 2 | ENSP00000426948.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250572Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135410
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1460258Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 726564
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4519G>A (p.D1507N) alteration is located in exon 28 (coding exon 28) of the RAPGEF6 gene. This alteration results from a G to A substitution at nucleotide position 4519, causing the aspartic acid (D) at amino acid position 1507 to be replaced by an asparagine (N). 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