11-32602839-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001008391.4(CCDC73):āc.3212C>Gā(p.Thr1071Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000025 in 1,601,614 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (ā ).
Frequency
Consequence
NM_001008391.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC73 | NM_001008391.4 | c.3212C>G | p.Thr1071Arg | missense_variant | 18/18 | ENST00000335185.10 | NP_001008392.2 | |
EIF3M | NM_006360.6 | c.*440G>C | 3_prime_UTR_variant | 11/11 | ENST00000531120.6 | NP_006351.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC73 | ENST00000335185.10 | c.3212C>G | p.Thr1071Arg | missense_variant | 18/18 | 2 | NM_001008391.4 | ENSP00000335325.5 | ||
EIF3M | ENST00000531120.6 | c.*440G>C | 3_prime_UTR_variant | 11/11 | 1 | NM_006360.6 | ENSP00000436049.1 | |||
CCDC73 | ENST00000528333.1 | c.317C>G | p.Thr106Arg | missense_variant | 2/2 | 3 | ENSP00000434365.1 | |||
EIF3M | ENST00000524896.5 | c.*440G>C | downstream_gene_variant | 2 | ENSP00000436787.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151898Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1449716Hom.: 0 Cov.: 29 AF XY: 0.00000139 AC XY: 1AN XY: 720824
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151898Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74174
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 18, 2023 | The c.3212C>G (p.T1071R) alteration is located in exon 18 (coding exon 17) of the CCDC73 gene. This alteration results from a C to G substitution at nucleotide position 3212, causing the threonine (T) at amino acid position 1071 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at