10-113876766-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM1PM2BP4_Strong
The NM_198514.4(NHLRC2):c.577A>G(p.Ile193Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000993 in 1,610,804 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_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.577A>G | p.Ile193Val | missense_variant | 3/11 | ENST00000369301.3 | |
NHLRC2 | XM_011539769.4 | c.577A>G | p.Ile193Val | missense_variant | 3/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NHLRC2 | ENST00000369301.3 | c.577A>G | p.Ile193Val | missense_variant | 3/11 | 2 | NM_198514.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250586Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135618
GnomAD4 exome AF: 0.00000891 AC: 13AN: 1458618Hom.: 0 Cov.: 29 AF XY: 0.0000124 AC XY: 9AN XY: 725842
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.577A>G (p.I193V) alteration is located in exon 3 (coding exon 3) of the NHLRC2 gene. This alteration results from a A to G substitution at nucleotide position 577, causing the isoleucine (I) at amino acid position 193 to be replaced by a valine (V). 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