3-141487085-T-TGGC
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PM4_SupportingBP6
The NM_006506.5(RASA2):c.13_15dupGCG(p.Ala5dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000435 in 1,356,370 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_006506.5 conservative_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RASA2 | NM_006506.5 | c.13_15dupGCG | p.Ala5dup | conservative_inframe_insertion | Exon 1 of 24 | ENST00000286364.9 | NP_006497.2 | |
RASA2 | NM_001303246.3 | c.13_15dupGCG | p.Ala5dup | conservative_inframe_insertion | Exon 1 of 25 | NP_001290175.1 | ||
RASA2 | NM_001303245.3 | c.13_15dupGCG | p.Ala5dup | conservative_inframe_insertion | Exon 1 of 24 | NP_001290174.1 | ||
RASA2 | XM_047448652.1 | c.13_15dupGCG | p.Ala5dup | conservative_inframe_insertion | Exon 1 of 17 | XP_047304608.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RASA2 | ENST00000286364.9 | c.13_15dupGCG | p.Ala5dup | conservative_inframe_insertion | Exon 1 of 24 | 1 | NM_006506.5 | ENSP00000286364.3 | ||
RASA2 | ENST00000515549.1 | n.13_15dupGCG | non_coding_transcript_exon_variant | Exon 1 of 5 | 4 | ENSP00000424293.1 |
Frequencies
GnomAD3 genomes AF: 0.0000534 AC: 8AN: 149682Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000359 AC: 2AN: 55636Hom.: 0 AF XY: 0.0000645 AC XY: 2AN XY: 31016
GnomAD4 exome AF: 0.0000423 AC: 51AN: 1206688Hom.: 0 Cov.: 30 AF XY: 0.0000558 AC XY: 33AN XY: 591886
GnomAD4 genome AF: 0.0000534 AC: 8AN: 149682Hom.: 0 Cov.: 32 AF XY: 0.0000411 AC XY: 3AN XY: 73044
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
This variant, c.13_15dup, results in the insertion of 1 amino acid(s) of the RASA2 protein (p.Ala5dup), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs747837865, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with RASA2-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
In-frame insertion in a repetitive region with no known function; Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at