chr2-117975261-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_019044.5(CCDC93):c.677C>T(p.Ala226Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000614 in 1,613,084 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_019044.5 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 |
---|---|---|---|---|---|---|---|
CCDC93 | NM_019044.5 | c.677C>T | p.Ala226Val | missense_variant | 9/24 | ENST00000376300.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC93 | ENST00000376300.7 | c.677C>T | p.Ala226Val | missense_variant | 9/24 | 1 | NM_019044.5 | P4 | |
CCDC93 | ENST00000319432.9 | c.674C>T | p.Ala225Val | missense_variant | 9/24 | 5 | A1 | ||
CCDC93 | ENST00000460781.1 | n.241C>T | non_coding_transcript_exon_variant | 5/10 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250724Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135564
GnomAD4 exome AF: 0.0000616 AC: 90AN: 1460880Hom.: 0 Cov.: 31 AF XY: 0.0000578 AC XY: 42AN XY: 726844
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.677C>T (p.A226V) alteration is located in exon 9 (coding exon 9) of the CCDC93 gene. This alteration results from a C to T substitution at nucleotide position 677, causing the alanine (A) at amino acid position 226 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