rs7913176
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_198514.4(NHLRC2):c.940G>A(p.Val314Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 1,608,448 control chromosomes in the GnomAD database, including 63,487 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_198514.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NHLRC2 | NM_198514.4 | c.940G>A | p.Val314Ile | missense_variant | 5/11 | ENST00000369301.3 | |
NHLRC2 | XM_011539769.4 | c.940G>A | p.Val314Ile | missense_variant | 5/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NHLRC2 | ENST00000369301.3 | c.940G>A | p.Val314Ile | missense_variant | 5/11 | 2 | NM_198514.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.250 AC: 37925AN: 151572Hom.: 5157 Cov.: 32
GnomAD3 exomes AF: 0.276 AC: 69339AN: 250812Hom.: 9987 AF XY: 0.273 AC XY: 37059AN XY: 135600
GnomAD4 exome AF: 0.279 AC: 406600AN: 1456756Hom.: 58325 Cov.: 30 AF XY: 0.277 AC XY: 201023AN XY: 724860
GnomAD4 genome ? AF: 0.250 AC: 37937AN: 151692Hom.: 5162 Cov.: 32 AF XY: 0.253 AC XY: 18745AN XY: 74144
ClinVar
Submissions by phenotype
NHLRC2-related condition Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at