chr10-100291345-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_016112.3(PKD2L1):c.1963G>A(p.Glu655Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,461,826 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_016112.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PKD2L1 | NM_016112.3 | c.1963G>A | p.Glu655Lys | missense_variant | 12/16 | ENST00000318222.4 | NP_057196.2 | |
PKD2L1 | NM_001253837.2 | c.1822G>A | p.Glu608Lys | missense_variant | 12/16 | NP_001240766.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PKD2L1 | ENST00000318222.4 | c.1963G>A | p.Glu655Lys | missense_variant | 12/16 | 1 | NM_016112.3 | ENSP00000325296.3 | ||
PKD2L1 | ENST00000528248.1 | n.*1703G>A | non_coding_transcript_exon_variant | 12/16 | 1 | ENSP00000436514.1 | ||||
PKD2L1 | ENST00000528248.1 | n.*1703G>A | 3_prime_UTR_variant | 12/16 | 1 | ENSP00000436514.1 | ||||
PKD2L1 | ENST00000465680.2 | c.104-2867G>A | intron_variant | 3 | ENSP00000434019.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251448Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135900
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461826Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727216
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 10, 2024 | The c.1963G>A (p.E655K) alteration is located in exon 12 (coding exon 12) of the PKD2L1 gene. This alteration results from a G to A substitution at nucleotide position 1963, causing the glutamic acid (E) at amino acid position 655 to be replaced by a lysine (K). 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