3-112638066-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_199511.3(CCDC80):c.1840G>A(p.Asp614Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000126 in 1,609,432 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_199511.3 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 |
---|---|---|---|---|---|---|---|
CCDC80 | NM_199511.3 | c.1840G>A | p.Asp614Asn | missense_variant | 2/8 | ENST00000206423.8 | |
CCDC80 | NM_199512.3 | c.1840G>A | p.Asp614Asn | missense_variant | 2/8 | ||
CCDC80 | XM_047447495.1 | c.1873G>A | p.Asp625Asn | missense_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC80 | ENST00000206423.8 | c.1840G>A | p.Asp614Asn | missense_variant | 2/8 | 1 | NM_199511.3 | P1 | |
CCDC80 | ENST00000439685.6 | c.1840G>A | p.Asp614Asn | missense_variant | 2/8 | 1 | P1 | ||
CCDC80 | ENST00000461431.1 | c.34G>A | p.Asp12Asn | missense_variant | 1/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000986 AC: 15AN: 152188Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000234 AC: 57AN: 244064Hom.: 1 AF XY: 0.000288 AC XY: 38AN XY: 131994
GnomAD4 exome AF: 0.000129 AC: 188AN: 1457126Hom.: 1 Cov.: 33 AF XY: 0.000170 AC XY: 123AN XY: 724712
GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152306Hom.: 0 Cov.: 31 AF XY: 0.0000806 AC XY: 6AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | The c.1840G>A (p.D614N) alteration is located in exon 2 (coding exon 1) of the CCDC80 gene. This alteration results from a G to A substitution at nucleotide position 1840, causing the aspartic acid (D) at amino acid position 614 to be replaced by an asparagine (N). 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