10-98208740-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001351015.2(R3HCC1L):c.626C>G(p.Thr209Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,614,126 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_001351015.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
R3HCC1L | NM_001351015.2 | c.626C>G | p.Thr209Ser | missense_variant | 5/10 | ENST00000298999.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
R3HCC1L | ENST00000298999.8 | c.626C>G | p.Thr209Ser | missense_variant | 5/10 | 5 | NM_001351015.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251092Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135690
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461798Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727202
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152328Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2023 | The c.626C>G (p.T209S) alteration is located in exon 4 (coding exon 1) of the R3HCC1L gene. This alteration results from a C to G substitution at nucleotide position 626, causing the threonine (T) at amino acid position 209 to be replaced by a serine (S). 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