6-31145061-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001105564.2(CCHCR1):c.1889G>A(p.Arg630Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000594 in 1,600,390 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001105564.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000355 AC: 54AN: 152100Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000798 AC: 19AN: 238234Hom.: 0 AF XY: 0.0000770 AC XY: 10AN XY: 129940
GnomAD4 exome AF: 0.0000283 AC: 41AN: 1448290Hom.: 0 Cov.: 35 AF XY: 0.0000333 AC XY: 24AN XY: 720236
GnomAD4 genome AF: 0.000355 AC: 54AN: 152100Hom.: 0 Cov.: 31 AF XY: 0.000619 AC XY: 46AN XY: 74278
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1889G>A (p.R630Q) alteration is located in exon 14 (coding exon 14) of the CCHCR1 gene. This alteration results from a G to A substitution at nucleotide position 1889, causing the arginine (R) at amino acid position 630 to be replaced by a glutamine (Q). 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