rs200797532
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017721.5(CC2D1A):c.1549G>A(p.Val517Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000261 in 1,614,014 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_017721.5 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 | UniProt |
---|---|---|---|---|---|---|---|
CC2D1A | NM_017721.5 | c.1549G>A | p.Val517Met | missense_variant | 14/29 | ENST00000318003.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CC2D1A | ENST00000318003.11 | c.1549G>A | p.Val517Met | missense_variant | 14/29 | 1 | NM_017721.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000177 AC: 27AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000116 AC: 29AN: 249096Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 135188
GnomAD4 exome AF: 0.000270 AC: 395AN: 1461806Hom.: 1 Cov.: 33 AF XY: 0.000230 AC XY: 167AN XY: 727206
GnomAD4 genome ? AF: 0.000177 AC: 27AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74352
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 24, 2014 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at