chr11-59655677-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_152716.3(PATL1):c.877C>T(p.Leu293Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00552 in 1,605,500 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_152716.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PATL1 | NM_152716.3 | c.877C>T | p.Leu293Phe | missense_variant | 8/19 | ENST00000300146.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PATL1 | ENST00000300146.10 | c.877C>T | p.Leu293Phe | missense_variant | 8/19 | 1 | NM_152716.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00386 AC: 587AN: 152118Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.00401 AC: 942AN: 235168Hom.: 5 AF XY: 0.00408 AC XY: 518AN XY: 127102
GnomAD4 exome AF: 0.00570 AC: 8285AN: 1453264Hom.: 29 Cov.: 31 AF XY: 0.00554 AC XY: 4000AN XY: 721930
GnomAD4 genome AF: 0.00384 AC: 585AN: 152236Hom.: 1 Cov.: 31 AF XY: 0.00360 AC XY: 268AN XY: 74444
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 08, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at