chr3-141487069-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006506.5(RASA2):c.-15G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000682 in 1,261,912 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
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RASA2 | NM_006506.5 | c.-15G>C | 5_prime_UTR_variant | Exon 1 of 24 | ENST00000286364.9 | NP_006497.2 | ||
RASA2 | NM_001303246.3 | c.-15G>C | 5_prime_UTR_variant | Exon 1 of 25 | NP_001290175.1 | |||
RASA2 | NM_001303245.3 | c.-15G>C | 5_prime_UTR_variant | Exon 1 of 24 | NP_001290174.1 | |||
RASA2 | XM_047448652.1 | c.-15G>C | 5_prime_UTR_variant | Exon 1 of 17 | XP_047304608.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RASA2 | ENST00000286364 | c.-15G>C | 5_prime_UTR_variant | Exon 1 of 24 | 1 | NM_006506.5 | ENSP00000286364.3 | |||
RASA2 | ENST00000515549.1 | n.-15G>C | non_coding_transcript_exon_variant | Exon 1 of 5 | 4 | ENSP00000424293.1 | ||||
RASA2 | ENST00000515549.1 | n.-15G>C | 5_prime_UTR_variant | Exon 1 of 5 | 4 | ENSP00000424293.1 |
Frequencies
GnomAD3 genomes AF: 0.0000733 AC: 11AN: 150044Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000634 AC: 1AN: 15774Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 8412
GnomAD4 exome AF: 0.0000675 AC: 75AN: 1111868Hom.: 0 Cov.: 30 AF XY: 0.0000668 AC XY: 36AN XY: 538734
GnomAD4 genome AF: 0.0000733 AC: 11AN: 150044Hom.: 0 Cov.: 32 AF XY: 0.0000273 AC XY: 2AN XY: 73230
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant summary: RASA2 c.-15G>C is located in the untranslated mRNA region upstream of the initiation codon. The variant allele was found at a frequency of 6.3e-05 in 15774 control chromosomes. 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>C 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