chr1-162854784-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001394065.1(CCDC190):c.887C>A(p.Ser296Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000994 in 1,609,946 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC190 | NM_001394065.1 | c.887C>A | p.Ser296Tyr | missense_variant | 4/4 | ENST00000367912.7 | |
CCDC190 | NM_178550.6 | c.890C>A | p.Ser297Tyr | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC190 | ENST00000367912.7 | c.887C>A | p.Ser296Tyr | missense_variant | 4/4 | 5 | NM_001394065.1 | A2 | |
CCDC190 | ENST00000524691.1 | n.152+848C>A | intron_variant, non_coding_transcript_variant | 1 | |||||
CCDC190 | ENST00000367910.5 | c.890C>A | p.Ser297Tyr | missense_variant | 4/4 | 2 | P4 | ||
CCDC190 | ENST00000367911.3 | c.890C>A | p.Ser297Tyr | missense_variant | 3/3 | 3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000566 AC: 14AN: 247264Hom.: 0 AF XY: 0.0000298 AC XY: 4AN XY: 134122
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1457760Hom.: 0 Cov.: 32 AF XY: 0.00000690 AC XY: 5AN XY: 724580
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2022 | The c.890C>A (p.S297Y) alteration is located in exon 4 (coding exon 3) of the CCDC190 gene. This alteration results from a C to A substitution at nucleotide position 890, causing the serine (S) at amino acid position 297 to be replaced by a tyrosine (Y). 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