chr17-44678945-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_144609.3(CCDC43):c.586A>G(p.Lys196Glu) variant causes a missense change. The variant allele was found at a frequency of 0.00000682 in 1,613,820 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K196Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_144609.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC43 | NM_144609.3 | c.586A>G | p.Lys196Glu | missense_variant | 5/5 | ENST00000315286.13 | |
CCDC43 | NM_001099225.2 | c.*62A>G | 3_prime_UTR_variant | 4/4 | |||
LOC105371792 | XR_934780.1 | upstream_gene_variant | |||||
LOC105371792 | XR_007065769.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC43 | ENST00000315286.13 | c.586A>G | p.Lys196Glu | missense_variant | 5/5 | 1 | NM_144609.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152122Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461698Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727130
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152122Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 27, 2022 | The c.586A>G (p.K196E) alteration is located in exon 5 (coding exon 5) of the CCDC43 gene. This alteration results from a A to G substitution at nucleotide position 586, causing the lysine (K) at amino acid position 196 to be replaced by a glutamic acid (E). 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