chr9-35660590-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_174923.3(CCDC107):āc.353C>Gā(p.Ala118Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000892 in 1,614,048 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (ā ).
Frequency
Consequence
NM_174923.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC107 | NM_174923.3 | c.353C>G | p.Ala118Gly | missense_variant | 4/5 | ENST00000426546.7 | |
ARHGEF39 | NM_032818.3 | c.*1397G>C | 3_prime_UTR_variant | 9/9 | ENST00000378387.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC107 | ENST00000426546.7 | c.353C>G | p.Ala118Gly | missense_variant | 4/5 | 1 | NM_174923.3 | A2 | |
ARHGEF39 | ENST00000378387.4 | c.*1397G>C | 3_prime_UTR_variant | 9/9 | 1 | NM_032818.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000994 AC: 25AN: 251448Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135912
GnomAD4 exome AF: 0.0000889 AC: 130AN: 1461886Hom.: 1 Cov.: 32 AF XY: 0.0000811 AC XY: 59AN XY: 727240
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 15, 2021 | The c.353C>G (p.A118G) alteration is located in exon 4 (coding exon 4) of the CCDC107 gene. This alteration results from a C to G substitution at nucleotide position 353, causing the alanine (A) at amino acid position 118 to be replaced by a glycine (G). 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