chr7-77259007-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020879.3(CCDC146):c.697C>A(p.His233Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,611,626 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (★).
Frequency
Consequence
NM_020879.3 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 | UniProt |
---|---|---|---|---|---|---|---|
CCDC146 | NM_020879.3 | c.697C>A | p.His233Asn | missense_variant | 7/19 | ENST00000285871.5 | |
LOC102723791 | XR_927688.3 | n.380-1752G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC146 | ENST00000285871.5 | c.697C>A | p.His233Asn | missense_variant | 7/19 | 1 | NM_020879.3 | P1 | |
CCDC146 | ENST00000461882.1 | n.333C>A | non_coding_transcript_exon_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152092Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250082Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135156
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1459534Hom.: 1 Cov.: 29 AF XY: 0.0000289 AC XY: 21AN XY: 726122
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152092Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2022 | The c.697C>A (p.H233N) alteration is located in exon 7 (coding exon 6) of the CCDC146 gene. This alteration results from a C to A substitution at nucleotide position 697, causing the histidine (H) at amino acid position 233 to be replaced by an asparagine (N). 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