rs117646559
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_033124.5(CCDC65):c.1021G>T(p.Asp341Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0113 in 1,610,524 control chromosomes in the GnomAD database, including 124 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 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. D341G) has been classified as Uncertain significance.
Frequency
Consequence
NM_033124.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC65 | NM_033124.5 | c.1021G>T | p.Asp341Tyr | missense_variant | 6/8 | ENST00000320516.5 | |
CCDC65 | NM_001286957.2 | c.592G>T | p.Asp198Tyr | missense_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC65 | ENST00000320516.5 | c.1021G>T | p.Asp341Tyr | missense_variant | 6/8 | 1 | NM_033124.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00815 AC: 1225AN: 150226Hom.: 7 Cov.: 31
GnomAD3 exomes AF: 0.00752 AC: 1887AN: 251054Hom.: 10 AF XY: 0.00780 AC XY: 1058AN XY: 135726
GnomAD4 exome AF: 0.0117 AC: 17033AN: 1460198Hom.: 117 Cov.: 31 AF XY: 0.0115 AC XY: 8355AN XY: 726540
GnomAD4 genome ? AF: 0.00814 AC: 1224AN: 150326Hom.: 7 Cov.: 31 AF XY: 0.00790 AC XY: 580AN XY: 73372
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia 27 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Mar 03, 2022 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 03, 2022 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | CCDC65: BP4, BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at