1-61875352-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001350145.3(PATJ):āc.2945C>Gā(p.Thr982Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000167 in 1,608,626 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 Likely benign (ā ).
Frequency
Consequence
NM_001350145.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PATJ | NM_001350145.3 | c.2945C>G | p.Thr982Ser | missense_variant | 21/44 | ENST00000642238.2 | NP_001337074.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PATJ | ENST00000642238.2 | c.2945C>G | p.Thr982Ser | missense_variant | 21/44 | NM_001350145.3 | ENSP00000494277.1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152142Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000691 AC: 17AN: 246068Hom.: 0 AF XY: 0.0000602 AC XY: 8AN XY: 132958
GnomAD4 exome AF: 0.000178 AC: 259AN: 1456484Hom.: 0 Cov.: 29 AF XY: 0.000145 AC XY: 105AN XY: 724456
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152142Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74320
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 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