5-87268321-TTTG-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_002890.3(RASA1):c.-122_-120del variant causes a 5 prime UTR change. The variant allele was found at a frequency of 0.000246 in 857,782 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00024 ( 0 hom. )
Consequence
RASA1
NM_002890.3 5_prime_UTR
NM_002890.3 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.62
Genes affected
RASA1 (HGNC:9871): (RAS p21 protein activator 1) The protein encoded by this gene is located in the cytoplasm and is part of the GAP1 family of GTPase-activating proteins. The gene product stimulates the GTPase activity of normal RAS p21 but not its oncogenic counterpart. Acting as a suppressor of RAS function, the protein enhances the weak intrinsic GTPase activity of RAS proteins resulting in the inactive GDP-bound form of RAS, thereby allowing control of cellular proliferation and differentiation. Mutations leading to changes in the binding sites of either protein are associated with basal cell carcinomas. Mutations also have been associated with hereditary capillary malformations (CM) with or without arteriovenous malformations (AVM) and Parkes Weber syndrome. Alternative splicing results in two isoforms where the shorter isoform, lacking the N-terminal hydrophobic region but retaining the same activity, appears to be abundantly expressed in placental but not adult tissues. [provided by RefSeq, May 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 5-87268321-TTTG-T is Benign according to our data. Variant chr5-87268321-TTTG-T is described in ClinVar as [Likely_benign]. Clinvar id is 354503.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000264 (37/140202) while in subpopulation EAS AF= 0.00783 (36/4598). AF 95% confidence interval is 0.00581. There are 0 homozygotes in gnomad4. There are 22 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 37 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RASA1 | NM_002890.3 | c.-122_-120del | 5_prime_UTR_variant | 1/25 | ENST00000274376.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RASA1 | ENST00000274376.11 | c.-122_-120del | 5_prime_UTR_variant | 1/25 | 1 | NM_002890.3 | P2 | ||
RASA1 | ENST00000515800.6 | c.-122_-120del | 5_prime_UTR_variant, NMD_transcript_variant | 1/26 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000264 AC: 37AN: 140092Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00100 AC: 49AN: 48824Hom.: 0 AF XY: 0.000685 AC XY: 17AN XY: 24802
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GnomAD4 exome AF: 0.000242 AC: 174AN: 717580Hom.: 0 AF XY: 0.000202 AC XY: 72AN XY: 356064
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Parkes Weber syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Capillary malformation-arteriovenous malformation 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at