10-12898458-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000378825.5(CCDC3):āc.771C>Gā(p.Ile257Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000683 in 1,611,010 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
ENST00000378825.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC3 | NM_031455.4 | c.771C>G | p.Ile257Met | missense_variant | 3/3 | ENST00000378825.5 | NP_113643.1 | |
CCDC3 | NM_001282658.2 | c.396C>G | p.Ile132Met | missense_variant | 7/7 | NP_001269587.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC3 | ENST00000378825.5 | c.771C>G | p.Ile257Met | missense_variant | 3/3 | 1 | NM_031455.4 | ENSP00000368102 | P1 | |
ENST00000649832.1 | n.511-54G>C | intron_variant, non_coding_transcript_variant | ||||||||
CCDC3 | ENST00000378839.1 | c.396C>G | p.Ile132Met | missense_variant | 7/7 | 2 | ENSP00000368116 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152256Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000407 AC: 1AN: 245648Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133930
GnomAD4 exome AF: 0.00000686 AC: 10AN: 1458754Hom.: 0 Cov.: 35 AF XY: 0.00000965 AC XY: 7AN XY: 725256
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2023 | The c.771C>G (p.I257M) alteration is located in exon 3 (coding exon 3) of the CCDC3 gene. This alteration results from a C to G substitution at nucleotide position 771, causing the isoleucine (I) at amino acid position 257 to be replaced by a methionine (M). 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