rs6573
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_002884.4(RAP1A):c.*366C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,412 control chromosomes in the GnomAD database, including 1,552 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.13 ( 1543 hom., cov: 32)
Exomes 𝑓: 0.20 ( 9 hom. )
Consequence
RAP1A
NM_002884.4 3_prime_UTR
NM_002884.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.83
Genes affected
RAP1A (HGNC:9855): (RAP1A, member of RAS oncogene family) This gene encodes a member of the Ras family of small GTPases. The encoded protein undergoes a change in conformational state and activity, depending on whether it is bound to GTP or GDP. This protein is activated by several types of guanine nucleotide exchange factors (GEFs), and inactivated by two groups of GTPase-activating proteins (GAPs). The activation status of the encoded protein is therefore affected by the balance of intracellular levels of GEFs and GAPs. The encoded protein regulates signaling pathways that affect cell proliferation and adhesion, and may play a role in tumor malignancy. Pseudogenes of this gene have been defined on chromosomes 14 and 17. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAP1A | NM_002884.4 | c.*366C>A | 3_prime_UTR_variant | 8/8 | ENST00000369709.4 | NP_002875.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAP1A | ENST00000369709.4 | c.*366C>A | 3_prime_UTR_variant | 8/8 | 1 | NM_002884.4 | ENSP00000358723 | P1 | ||
RAP1A | ENST00000356415.5 | c.*366C>A | 3_prime_UTR_variant | 8/8 | 1 | ENSP00000348786 | P1 | |||
RAP1A | ENST00000687939.1 | c.*366C>A | 3_prime_UTR_variant | 9/9 | ENSP00000509234 | P1 | ||||
INKA2 | ENST00000527570.1 | n.219-26084G>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.126 AC: 19174AN: 151864Hom.: 1537 Cov.: 32
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GnomAD4 exome AF: 0.195 AC: 84AN: 430Hom.: 9 Cov.: 0 AF XY: 0.198 AC XY: 51AN XY: 258
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GnomAD4 genome AF: 0.126 AC: 19190AN: 151982Hom.: 1543 Cov.: 32 AF XY: 0.128 AC XY: 9504AN XY: 74282
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at