rs7976407
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001301202.2(RASAL1):c.66-51T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 1,440,484 control chromosomes in the GnomAD database, including 10,189 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 0.14 ( 1668 hom., cov: 31)
Exomes 𝑓: 0.10 ( 8521 hom. )
Consequence
RASAL1
NM_001301202.2 intron
NM_001301202.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.49
Genes affected
RASAL1 (HGNC:9873): (RAS protein activator like 1) The protein encoded by this gene is member of the GAP1 family of GTPase-activating proteins. These proteins stimulate 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. This particular family member contains domains which are characteristic of the GAP1 subfamily of RasGAP proteins but, in contrast to the other GAP1 family members, this protein is strongly and selectively expressed in endocrine tissues. Alternatively spliced transcript variants that encode different isoforms have been described [provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RASAL1 | NM_001301202.2 | c.66-51T>C | intron_variant | ENST00000548055.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RASAL1 | ENST00000548055.2 | c.66-51T>C | intron_variant | 1 | NM_001301202.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.135 AC: 20498AN: 151884Hom.: 1651 Cov.: 31
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GnomAD3 exomes AF: 0.123 AC: 28813AN: 234592Hom.: 2152 AF XY: 0.124 AC XY: 15641AN XY: 126422
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GnomAD4 exome AF: 0.104 AC: 134572AN: 1288482Hom.: 8521 Cov.: 18 AF XY: 0.107 AC XY: 69389AN XY: 648402
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GnomAD4 genome ? AF: 0.135 AC: 20550AN: 152002Hom.: 1668 Cov.: 31 AF XY: 0.137 AC XY: 10201AN XY: 74286
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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