rs150501049
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016340.6(RAPGEF6):āc.4112G>Cā(p.Ser1371Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S1371N) has been classified 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.4112G>C | p.Ser1371Thr | missense_variant | Exon 26 of 28 | ENST00000509018.6 | NP_057424.3 | |
RAPGEF6 | NM_001164386.2 | c.4136G>C | p.Ser1379Thr | missense_variant | Exon 27 of 29 | NP_001157858.1 | ||
RAPGEF6 | NM_001164387.2 | c.4151G>C | p.Ser1384Thr | missense_variant | Exon 28 of 29 | NP_001157859.1 | ||
RAPGEF6 | NM_001164388.2 | c.4136G>C | p.Ser1379Thr | missense_variant | Exon 27 of 28 | NP_001157860.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAPGEF6 | ENST00000509018.6 | c.4112G>C | p.Ser1371Thr | missense_variant | Exon 26 of 28 | 1 | NM_016340.6 | ENSP00000421684.1 | ||
ENSG00000273217 | ENST00000514667.1 | c.4262G>C | p.Ser1421Thr | missense_variant | Exon 27 of 29 | 2 | ENSP00000426948.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461888Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 727244
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.