chr1-162859630-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001394065.1(CCDC190):c.17T>C(p.Val6Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,613,336 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 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.17T>C | p.Val6Ala | missense_variant | 2/4 | ENST00000367912.7 | |
CCDC190 | NM_178550.6 | c.17T>C | p.Val6Ala | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC190 | ENST00000367912.7 | c.17T>C | p.Val6Ala | missense_variant | 2/4 | 5 | NM_001394065.1 | A2 | |
CCDC190 | ENST00000367910.5 | c.17T>C | p.Val6Ala | missense_variant | 2/4 | 2 | P4 | ||
CCDC190 | ENST00000367911.3 | c.17T>C | p.Val6Ala | missense_variant | 1/3 | 3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000101 AC: 25AN: 248192Hom.: 0 AF XY: 0.0000669 AC XY: 9AN XY: 134604
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461144Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 726828
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.17T>C (p.V6A) alteration is located in exon 2 (coding exon 1) of the CCDC190 gene. This alteration results from a T to C substitution at nucleotide position 17, causing the valine (V) at amino acid position 6 to be replaced by an alanine (A). 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