chr9-122855389-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001100588.3(RC3H2):c.2610C>G(p.Asp870Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000172 in 1,612,776 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001100588.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RC3H2 | NM_001100588.3 | c.2610C>G | p.Asp870Glu | missense_variant | 15/21 | ENST00000357244.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RC3H2 | ENST00000357244.7 | c.2610C>G | p.Asp870Glu | missense_variant | 15/21 | 5 | NM_001100588.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000493 AC: 75AN: 152134Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000241 AC: 60AN: 249472Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135384
GnomAD4 exome AF: 0.000140 AC: 204AN: 1460524Hom.: 0 Cov.: 32 AF XY: 0.000131 AC XY: 95AN XY: 726620
GnomAD4 genome ? AF: 0.000479 AC: 73AN: 152252Hom.: 1 Cov.: 32 AF XY: 0.000510 AC XY: 38AN XY: 74444
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.2610C>G (p.D870E) alteration is located in exon 15 (coding exon 14) of the RC3H2 gene. This alteration results from a C to G substitution at nucleotide position 2610, causing the aspartic acid (D) at amino acid position 870 to be replaced by a glutamic acid (E). 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