chr9-131588921-T-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_001377935.1(RAPGEF1):c.2933A>G(p.Asn978Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,613,740 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N978T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001377935.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAPGEF1 | NM_001377935.1 | c.2933A>G | p.Asn978Ser | missense_variant | 20/27 | ENST00000683357.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAPGEF1 | ENST00000683357.1 | c.2933A>G | p.Asn978Ser | missense_variant | 20/27 | NM_001377935.1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152088Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249096Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135144
GnomAD4 exome AF: 0.0000390 AC: 57AN: 1461652Hom.: 0 Cov.: 31 AF XY: 0.0000399 AC XY: 29AN XY: 727114
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152088Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74302
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at