7-4799386-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_018059.5(RADIL):c.3220C>T(p.Pro1074Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,584 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018059.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RADIL | NM_018059.5 | c.3220C>T | p.Pro1074Ser | missense_variant | 15/15 | ENST00000399583.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RADIL | ENST00000399583.4 | c.3220C>T | p.Pro1074Ser | missense_variant | 15/15 | 5 | NM_018059.5 | P1 | |
RADIL | ENST00000472999.5 | n.1244C>T | non_coding_transcript_exon_variant | 5/5 | 1 | ||||
RADIL | ENST00000473130.5 | n.1831C>T | non_coding_transcript_exon_variant | 11/11 | 2 | ||||
RADIL | ENST00000445392.5 | c.*1991C>T | 3_prime_UTR_variant, NMD_transcript_variant | 15/15 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461418Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727012
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | The c.3220C>T (p.P1074S) alteration is located in exon 15 (coding exon 14) of the RADIL gene. This alteration results from a C to T substitution at nucleotide position 3220, causing the proline (P) at amino acid position 1074 to be replaced by a serine (S). 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