rs786204221
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000297.4(PKD2):c.70C>T(p.Pro24Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000822 in 1,167,354 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P24L) has been classified as Likely benign.
Frequency
Consequence
NM_000297.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKD2 | NM_000297.4 | c.70C>T | p.Pro24Ser | missense_variant | 1/15 | ENST00000237596.7 | |
PKD2 | XM_011532028.3 | c.70C>T | p.Pro24Ser | missense_variant | 1/14 | ||
PKD2 | NR_156488.2 | n.169C>T | non_coding_transcript_exon_variant | 1/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKD2 | ENST00000237596.7 | c.70C>T | p.Pro24Ser | missense_variant | 1/15 | 1 | NM_000297.4 | P1 | |
ENST00000662475.1 | n.112+563G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000101 AC: 15AN: 148720Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000841 AC: 9AN: 10696Hom.: 0 AF XY: 0.000628 AC XY: 4AN XY: 6368
GnomAD4 exome AF: 0.0000795 AC: 81AN: 1018634Hom.: 0 Cov.: 29 AF XY: 0.0000905 AC XY: 44AN XY: 486388
GnomAD4 genome ? AF: 0.000101 AC: 15AN: 148720Hom.: 0 Cov.: 32 AF XY: 0.0000828 AC XY: 6AN XY: 72446
ClinVar
Submissions by phenotype
Autosomal dominant polycystic kidney disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
PKD2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 23, 2022 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at