chr15-44668999-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001387263.1(PATL2):c.1205G>A(p.Arg402Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000484 in 1,548,254 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001387263.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PATL2 | NM_001387263.1 | c.1205G>A | p.Arg402Gln | missense_variant | 14/18 | ENST00000682850.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PATL2 | ENST00000682850.1 | c.1205G>A | p.Arg402Gln | missense_variant | 14/18 | NM_001387263.1 | A2 | ||
PATL2 | ENST00000434130.6 | c.1205G>A | p.Arg402Gln | missense_variant | 12/16 | 5 | A2 | ||
PATL2 | ENST00000560780.1 | c.638G>A | p.Arg213Gln | missense_variant | 11/15 | 2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000106 AC: 16AN: 151264Hom.: 0 AF XY: 0.0000873 AC XY: 7AN XY: 80168
GnomAD4 exome AF: 0.0000501 AC: 70AN: 1395970Hom.: 1 Cov.: 32 AF XY: 0.0000465 AC XY: 32AN XY: 688256
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74470
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2023 | PATL2: PM2, BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at