chr16-81141306-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The ENST00000525539.5(PKD1L2):c.5408C>A(p.Ala1803Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000241 in 1,534,912 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 5/6 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000525539.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKD1L2 | NR_126532.3 | n.5423C>A | non_coding_transcript_exon_variant | 31/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKD1L2 | ENST00000525539.5 | c.5408C>A | p.Ala1803Glu | missense_variant | 31/43 | 1 | |||
PKD1L2 | ENST00000533478.5 | c.3353C>A | p.Ala1118Glu | missense_variant | 20/32 | 1 | |||
PKD1L2 | ENST00000530363.5 | n.194C>A | non_coding_transcript_exon_variant | 1/6 | 1 | ||||
PKD1L2 | ENST00000299598.11 | n.4805C>A | non_coding_transcript_exon_variant | 21/25 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000890 AC: 13AN: 146036Hom.: 0 AF XY: 0.0000636 AC XY: 5AN XY: 78648
GnomAD4 exome AF: 0.0000181 AC: 25AN: 1382698Hom.: 0 Cov.: 30 AF XY: 0.00000879 AC XY: 6AN XY: 682388
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 26, 2021 | The c.5408C>A (p.A1803E) alteration is located in exon 31 (coding exon 31) of the PKD1L2 gene. This alteration results from a C to A substitution at nucleotide position 5408, causing the alanine (A) at amino acid position 1803 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at