chr11-59639340-T-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_152716.3(PATL1):c.2093A>T(p.Asp698Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000342 in 1,550,690 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_152716.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PATL1 | NM_152716.3 | c.2093A>T | p.Asp698Val | missense_variant | 17/19 | ENST00000300146.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PATL1 | ENST00000300146.10 | c.2093A>T | p.Asp698Val | missense_variant | 17/19 | 1 | NM_152716.3 | P1 | |
ENST00000661394.1 | n.597T>A | non_coding_transcript_exon_variant | 5/5 | ||||||
ENST00000531108.1 | n.238T>A | non_coding_transcript_exon_variant | 4/4 | 3 | |||||
ENST00000531311.1 | n.80T>A | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000447 AC: 7AN: 156622Hom.: 0 AF XY: 0.0000363 AC XY: 3AN XY: 82658
GnomAD4 exome AF: 0.0000336 AC: 47AN: 1398518Hom.: 0 Cov.: 31 AF XY: 0.0000348 AC XY: 24AN XY: 689786
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74352
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at