1-162855109-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001394065.1(CCDC190):c.562A>G(p.Ile188Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,614,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001394065.1 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 |
---|---|---|---|---|---|---|---|
CCDC190 | NM_001394065.1 | c.562A>G | p.Ile188Val | missense_variant | 4/4 | ENST00000367912.7 | |
CCDC190 | NM_178550.6 | c.565A>G | p.Ile189Val | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC190 | ENST00000367912.7 | c.562A>G | p.Ile188Val | missense_variant | 4/4 | 5 | NM_001394065.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249176Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135188
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461664Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727118
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.565A>G (p.I189V) alteration is located in exon 4 (coding exon 3) of the CCDC190 gene. This alteration results from a A to G substitution at nucleotide position 565, causing the isoleucine (I) at amino acid position 189 to be replaced by a valine (V). 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