chr7-158650893-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017760.7(NCAPG2):c.3014G>A(p.Arg1005Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,613,890 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 (★).
Frequency
Consequence
NM_017760.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152076Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000361 AC: 9AN: 249338Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135278
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461696Hom.: 0 Cov.: 30 AF XY: 0.0000234 AC XY: 17AN XY: 727154
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74412
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3014G>A (p.R1005Q) alteration is located in exon 24 (coding exon 23) of the NCAPG2 gene. This alteration results from a G to A substitution at nucleotide position 3014, causing the arginine (R) at amino acid position 1005 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