chr1-23961597-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017761.4(PNRC2):āc.140A>Gā(p.His47Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000589 in 1,613,810 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_017761.4 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 |
---|---|---|---|---|---|---|---|
PNRC2 | NM_017761.4 | c.140A>G | p.His47Arg | missense_variant | 3/3 | ENST00000334351.8 | |
PNRC2 | XM_017001691.1 | c.140A>G | p.His47Arg | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNRC2 | ENST00000334351.8 | c.140A>G | p.His47Arg | missense_variant | 3/3 | 1 | NM_017761.4 | P1 | |
PNRC2 | ENST00000374468.1 | c.140A>G | p.His47Arg | missense_variant | 3/3 | 2 | P1 | ||
PNRC2 | ENST00000647887.1 | c.140A>G | p.His47Arg | missense_variant | 4/4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000604 AC: 92AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000329 AC: 13AN: 39496Hom.: 0 AF XY: 0.000301 AC XY: 6AN XY: 19922
GnomAD4 exome AF: 0.000587 AC: 858AN: 1461594Hom.: 0 Cov.: 33 AF XY: 0.000582 AC XY: 423AN XY: 727108
GnomAD4 genome AF: 0.000604 AC: 92AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.000565 AC XY: 42AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 27, 2022 | The c.140A>G (p.H47R) alteration is located in exon 3 (coding exon 1) of the PNRC2 gene. This alteration results from a A to G substitution at nucleotide position 140, causing the histidine (H) at amino acid position 47 to be replaced by an arginine (R). 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