chr22-30373697-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001017437.5(CCDC157):c.1436G>A(p.Arg479Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000618 in 1,552,976 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001017437.5 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 |
---|---|---|---|---|---|---|---|
CCDC157 | NM_001017437.5 | c.1436G>A | p.Arg479Gln | missense_variant | 8/12 | ENST00000338306.8 | |
KIAA1656 | NR_046312.1 | n.2719C>T | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC157 | ENST00000338306.8 | c.1436G>A | p.Arg479Gln | missense_variant | 8/12 | 5 | NM_001017437.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000525 AC: 8AN: 152240Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000101 AC: 16AN: 158614Hom.: 0 AF XY: 0.000107 AC XY: 9AN XY: 84074
GnomAD4 exome AF: 0.0000628 AC: 88AN: 1400736Hom.: 0 Cov.: 32 AF XY: 0.0000665 AC XY: 46AN XY: 691296
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152240Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2022 | The c.1436G>A (p.R479Q) alteration is located in exon 8 (coding exon 6) of the CCDC157 gene. This alteration results from a G to A substitution at nucleotide position 1436, causing the arginine (R) at amino acid position 479 to be replaced by a glutamine (Q). 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