19-19542611-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153221.2(CILP2):c.829G>A(p.Gly277Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,614,016 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153221.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CILP2 | NM_153221.2 | c.829G>A | p.Gly277Arg | missense_variant | 5/8 | ENST00000291495.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CILP2 | ENST00000291495.5 | c.829G>A | p.Gly277Arg | missense_variant | 5/8 | 1 | NM_153221.2 | P2 | |
CILP2 | ENST00000586018.5 | c.847G>A | p.Gly283Arg | missense_variant | 5/8 | 2 | A1 | ||
CILP2 | ENST00000588333.2 | n.519G>A | non_coding_transcript_exon_variant | 3/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251096Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135738
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461792Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727208
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74370
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at