1-42589344-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001395517.1(CCDC30):āc.1709A>Cā(p.Asp570Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,609,826 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001395517.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC30 | NM_001395517.1 | c.1709A>C | p.Asp570Ala | missense_variant | 14/21 | ENST00000657597.2 | |
LOC124904162 | XR_007066034.1 | n.77-18184T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC30 | ENST00000657597.2 | c.1709A>C | p.Asp570Ala | missense_variant | 14/21 | NM_001395517.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000645 AC: 16AN: 248022Hom.: 0 AF XY: 0.0000672 AC XY: 9AN XY: 133940
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1457654Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 724838
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 05, 2023 | The c.1244A>C (p.D415A) alteration is located in exon 9 (coding exon 8) of the CCDC30 gene. This alteration results from a A to C substitution at nucleotide position 1244, causing the aspartic acid (D) at amino acid position 415 to be replaced by an alanine (A). 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