chr16-722985-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001378030.1(CCDC78):c.1238G>A(p.Arg413Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000298 in 1,612,442 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict 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. R413W) has been classified as Likely benign.
Frequency
Consequence
NM_001378030.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC78 | NM_001378030.1 | c.1238G>A | p.Arg413Gln | missense_variant | 13/14 | ENST00000345165.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC78 | ENST00000345165.10 | c.1238G>A | p.Arg413Gln | missense_variant | 13/14 | 5 | NM_001378030.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00160 AC: 244AN: 152218Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.000385 AC: 96AN: 249502Hom.: 0 AF XY: 0.000288 AC XY: 39AN XY: 135488
GnomAD4 exome AF: 0.000163 AC: 238AN: 1460106Hom.: 0 Cov.: 34 AF XY: 0.000134 AC XY: 97AN XY: 726366
GnomAD4 genome AF: 0.00159 AC: 242AN: 152336Hom.: 1 Cov.: 34 AF XY: 0.00142 AC XY: 106AN XY: 74488
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Aug 19, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 23, 2019 | - - |
Congenital myopathy with internal nuclei and atypical cores Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 09, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at