16-81130486-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000525539.5(PKD1L2):c.6016G>C(p.Val2006Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000276 in 1,450,614 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PKD1L2 | NR_126532.3 | n.6031G>C | non_coding_transcript_exon_variant | Exon 35 of 43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PKD1L2 | ENST00000525539.5 | c.6016G>C | p.Val2006Leu | missense_variant | Exon 35 of 43 | 1 | ENSP00000434417.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000433 AC: 1AN: 230910Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 124928
GnomAD4 exome AF: 0.00000276 AC: 4AN: 1450614Hom.: 0 Cov.: 30 AF XY: 0.00000278 AC XY: 2AN XY: 720342
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.6016G>C (p.V2006L) alteration is located in exon 35 (coding exon 35) of the PKD1L2 gene. This alteration results from a G to C substitution at nucleotide position 6016, causing the valine (V) at amino acid position 2006 to be replaced by a leucine (L). 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