chr7-77256501-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020879.3(CCDC146):c.676G>A(p.Val226Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000475 in 1,600,730 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC146 | NM_020879.3 | c.676G>A | p.Val226Ile | missense_variant | 6/19 | ENST00000285871.5 | |
LOC102723791 | XR_927688.3 | n.434+700C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC146 | ENST00000285871.5 | c.676G>A | p.Val226Ile | missense_variant | 6/19 | 1 | NM_020879.3 | P1 | |
ENST00000476561.2 | n.272+700C>T | intron_variant, non_coding_transcript_variant | 4 | ||||||
CCDC146 | ENST00000461882.1 | n.312G>A | non_coding_transcript_exon_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000501 AC: 12AN: 239432Hom.: 0 AF XY: 0.0000540 AC XY: 7AN XY: 129558
GnomAD4 exome AF: 0.0000428 AC: 62AN: 1448516Hom.: 0 Cov.: 30 AF XY: 0.0000458 AC XY: 33AN XY: 720476
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2021 | The c.676G>A (p.V226I) alteration is located in exon 6 (coding exon 5) of the CCDC146 gene. This alteration results from a G to A substitution at nucleotide position 676, causing the valine (V) at amino acid position 226 to be replaced by an isoleucine (I). 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