NM_001008391.4:c.3125G>C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001008391.4(CCDC73):c.3125G>C(p.Ser1042Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,136 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S1042R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001008391.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC73 | ENST00000335185.10 | c.3125G>C | p.Ser1042Thr | missense_variant | Exon 18 of 18 | 2 | NM_001008391.4 | ENSP00000335325.5 | ||
EIF3M | ENST00000531120.6 | c.*527C>G | 3_prime_UTR_variant | Exon 11 of 11 | 1 | NM_006360.6 | ENSP00000436049.1 | |||
CCDC73 | ENST00000528333.1 | c.230G>C | p.Ser77Thr | missense_variant | Exon 2 of 2 | 3 | ENSP00000434365.1 | |||
EIF3M | ENST00000524896.5 | c.*527C>G | downstream_gene_variant | 2 | ENSP00000436787.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249156Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135174
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460990Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726808
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3125G>C (p.S1042T) alteration is located in exon 18 (coding exon 17) of the CCDC73 gene. This alteration results from a G to C substitution at nucleotide position 3125, causing the serine (S) at amino acid position 1042 to be replaced by a threonine (T). 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