10-100291354-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016112.3(PKD2L1):c.1954A>C(p.Ile652Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PKD2L1 | ENST00000318222.4 | c.1954A>C | p.Ile652Leu | missense_variant | 12/16 | 1 | NM_016112.3 | ENSP00000325296.3 | ||
PKD2L1 | ENST00000528248.1 | n.*1694A>C | non_coding_transcript_exon_variant | 12/16 | 1 | ENSP00000436514.1 | ||||
PKD2L1 | ENST00000528248.1 | n.*1694A>C | 3_prime_UTR_variant | 12/16 | 1 | ENSP00000436514.1 | ||||
PKD2L1 | ENST00000465680.2 | c.104-2876A>C | intron_variant | 3 | ENSP00000434019.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2023 | The c.1954A>C (p.I652L) alteration is located in exon 12 (coding exon 12) of the PKD2L1 gene. This alteration results from a A to C substitution at nucleotide position 1954, causing the isoleucine (I) at amino acid position 652 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
Publications
No publications associated with this variant yet.