10-100294952-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_016112.3(PKD2L1):c.1528A>C(p.Ile510Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,102 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016112.3 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 |
---|---|---|---|---|---|---|---|
PKD2L1 | NM_016112.3 | c.1528A>C | p.Ile510Leu | missense_variant | 8/16 | ENST00000318222.4 | |
PKD2L1 | NM_001253837.2 | c.1387A>C | p.Ile463Leu | missense_variant | 8/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKD2L1 | ENST00000318222.4 | c.1528A>C | p.Ile510Leu | missense_variant | 8/16 | 1 | NM_016112.3 | P1 | |
PKD2L1 | ENST00000528248.1 | c.*1268A>C | 3_prime_UTR_variant, NMD_transcript_variant | 8/16 | 1 | ||||
PKD2L1 | ENST00000465680.2 | c.105-6474A>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152156Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1460946Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726746
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152156Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2022 | The c.1528A>C (p.I510L) alteration is located in exon 8 (coding exon 8) of the PKD2L1 gene. This alteration results from a A to C substitution at nucleotide position 1528, causing the isoleucine (I) at amino acid position 510 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