chr1-2589029-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_152371.5(PRXL2B):c.568G>A(p.Asp190Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000302 in 1,612,654 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_152371.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRXL2B | NM_152371.5 | c.568G>A | p.Asp190Asn | missense_variant | 6/7 | ENST00000419916.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRXL2B | ENST00000419916.8 | c.568G>A | p.Asp190Asn | missense_variant | 6/7 | 1 | NM_152371.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000190 AC: 29AN: 152236Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000193 AC: 48AN: 248724Hom.: 0 AF XY: 0.000237 AC XY: 32AN XY: 135154
GnomAD4 exome AF: 0.000314 AC: 458AN: 1460418Hom.: 0 Cov.: 34 AF XY: 0.000307 AC XY: 223AN XY: 726572
GnomAD4 genome ? AF: 0.000190 AC: 29AN: 152236Hom.: 0 Cov.: 34 AF XY: 0.000202 AC XY: 15AN XY: 74380
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at