rs374749282
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_001378030.1(CCDC78):c.1276G>A(p.Glu426Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000148 in 1,612,246 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E426A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001378030.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC78 | NM_001378030.1 | c.1276G>A | p.Glu426Lys | missense_variant | 13/14 | ENST00000345165.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC78 | ENST00000345165.10 | c.1276G>A | p.Glu426Lys | missense_variant | 13/14 | 5 | NM_001378030.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152220Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000681 AC: 17AN: 249560Hom.: 0 AF XY: 0.0000812 AC XY: 11AN XY: 135490
GnomAD4 exome AF: 0.000158 AC: 231AN: 1460026Hom.: 0 Cov.: 34 AF XY: 0.000154 AC XY: 112AN XY: 726310
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152220Hom.: 0 Cov.: 34 AF XY: 0.0000538 AC XY: 4AN XY: 74360
ClinVar
Submissions by phenotype
Congenital myopathy with internal nuclei and atypical cores Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at