17-44901064-T-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_213607.3(CCDC103):c.66T>C(p.Ala22=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 1,601,342 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 (★). Synonymous variant affecting the same amino acid position (i.e. A22A) has been classified as Likely benign.
Frequency
Consequence
NM_213607.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC103 | NM_213607.3 | c.66T>C | p.Ala22= | synonymous_variant | 2/4 | ENST00000417826.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC103 | ENST00000417826.3 | c.66T>C | p.Ala22= | synonymous_variant | 2/4 | 1 | NM_213607.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152276Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000169 AC: 4AN: 236756Hom.: 0 AF XY: 0.00000778 AC XY: 1AN XY: 128592
GnomAD4 exome AF: 0.00000828 AC: 12AN: 1449066Hom.: 0 Cov.: 31 AF XY: 0.00000555 AC XY: 4AN XY: 721122
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152276Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74394
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 14, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at