19-48720995-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_017805.3(RASIP1):c.2695G>A(p.Asp899Asn) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000692 in 1,444,182 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017805.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RASIP1 | ENST00000222145.9 | c.2695G>A | p.Asp899Asn | missense_variant, splice_region_variant | Exon 12 of 12 | 1 | NM_017805.3 | ENSP00000222145.3 | ||
RASIP1 | ENST00000601530.1 | n.1189G>A | splice_region_variant, non_coding_transcript_exon_variant | Exon 4 of 4 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000692 AC: 10AN: 1444182Hom.: 0 Cov.: 31 AF XY: 0.00000419 AC XY: 3AN XY: 716768
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2695G>A (p.D899N) alteration is located in exon 12 (coding exon 11) of the RASIP1 gene. This alteration results from a G to A substitution at nucleotide position 2695, causing the aspartic acid (D) at amino acid position 899 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at