1-162855352-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001394065.1(CCDC190):c.319G>A(p.Ala107Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000206 in 1,598,072 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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC190 | ENST00000367912.7 | c.319G>A | p.Ala107Thr | missense_variant | Exon 4 of 4 | 5 | NM_001394065.1 | ENSP00000356888.3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152074Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000857 AC: 2AN: 233290Hom.: 0 AF XY: 0.0000156 AC XY: 2AN XY: 127832
GnomAD4 exome AF: 0.0000207 AC: 30AN: 1445998Hom.: 0 Cov.: 32 AF XY: 0.0000139 AC XY: 10AN XY: 719460
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74288
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.322G>A (p.A108T) alteration is located in exon 4 (coding exon 3) of the CCDC190 gene. This alteration results from a G to A substitution at nucleotide position 322, causing the alanine (A) at amino acid position 108 to be replaced by a threonine (T). 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