chr10-113879589-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198514.4(NHLRC2):c.803G>C(p.Arg268Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000562 in 1,601,726 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198514.4 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 |
---|---|---|---|---|---|---|---|
NHLRC2 | NM_198514.4 | c.803G>C | p.Arg268Thr | missense_variant | 4/11 | ENST00000369301.3 | |
NHLRC2 | XM_011539769.4 | c.803G>C | p.Arg268Thr | missense_variant | 4/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NHLRC2 | ENST00000369301.3 | c.803G>C | p.Arg268Thr | missense_variant | 4/11 | 2 | NM_198514.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152024Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000165 AC: 4AN: 242030Hom.: 0 AF XY: 0.0000229 AC XY: 3AN XY: 131216
GnomAD4 exome AF: 0.00000414 AC: 6AN: 1449584Hom.: 0 Cov.: 28 AF XY: 0.00000139 AC XY: 1AN XY: 721242
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74370
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 27, 2023 | The c.803G>C (p.R268T) alteration is located in exon 4 (coding exon 4) of the NHLRC2 gene. This alteration results from a G to C substitution at nucleotide position 803, causing the arginine (R) at amino acid position 268 to be replaced by a threonine (T). 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