3-141487069-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006506.5(RASA2):c.-15G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00008 in 1,261,914 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006506.5 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RASA2 | ENST00000286364 | c.-15G>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 24 | 1 | NM_006506.5 | ENSP00000286364.3 | |||
RASA2 | ENST00000286364 | c.-15G>T | 5_prime_UTR_variant | Exon 1 of 24 | 1 | NM_006506.5 | ENSP00000286364.3 |
Frequencies
GnomAD3 genomes AF: 0.000280 AC: 42AN: 150044Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000531 AC: 59AN: 1111870Hom.: 0 Cov.: 30 AF XY: 0.0000408 AC XY: 22AN XY: 538736
GnomAD4 genome AF: 0.000280 AC: 42AN: 150044Hom.: 0 Cov.: 32 AF XY: 0.000191 AC XY: 14AN XY: 73230
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant summary: RASA2 c.-15G>T is located in the untranslated mRNA region upstream of the initiation codon. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00018 in 43946 control chromosomes (gnomAD, genomes dataset). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.-15G>T in individuals affected with Noonan Syndrome and Related Conditions and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at