chr16-724193-G-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001378030.1(CCDC78):c.966C>A(p.Asn322Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00392 in 1,597,364 control chromosomes in the GnomAD database, including 43 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001378030.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC78 | NM_001378030.1 | c.966C>A | p.Asn322Lys | missense_variant | 10/14 | ENST00000345165.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC78 | ENST00000345165.10 | c.966C>A | p.Asn322Lys | missense_variant | 10/14 | 5 | NM_001378030.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00253 AC: 385AN: 152208Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00376 AC: 885AN: 235528Hom.: 17 AF XY: 0.00456 AC XY: 581AN XY: 127412
GnomAD4 exome AF: 0.00407 AC: 5880AN: 1445038Hom.: 42 Cov.: 35 AF XY: 0.00440 AC XY: 3156AN XY: 717322
GnomAD4 genome AF: 0.00253 AC: 385AN: 152326Hom.: 1 Cov.: 33 AF XY: 0.00260 AC XY: 194AN XY: 74484
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 24, 2014 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 18, 2021 | - - |
Congenital myopathy with internal nuclei and atypical cores Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at