chr4-88007803-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

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

Genomes: 𝑓 0.00010 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000080 ( 0 hom. )

Consequence

PKD2
NM_000297.4 missense

Scores

2
1
16

Clinical Significance

Likely benign criteria provided, single submitter B:2

Conservation

PhyloP100: -1.31
Variant links:
Genes affected
PKD2 (HGNC:9009): (polycystin 2, transient receptor potential cation channel) This gene encodes a member of the polycystin protein family. The encoded protein is a multi-pass membrane protein that functions as a calcium permeable cation channel, and is involved in calcium transport and calcium signaling in renal epithelial cells. This protein interacts with polycystin 1, and they may be partners in a common signaling cascade involved in tubular morphogenesis. Mutations in this gene are associated with autosomal dominant polycystic kidney disease type 2. [provided by RefSeq, Mar 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.005635977).
BP6
Variant 4-88007803-C-T is Benign according to our data. Variant chr4-88007803-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 188333.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.0000795 (81/1018634) while in subpopulation AMR AF= 0.00108 (9/8314). AF 95% confidence interval is 0.000564. There are 0 homozygotes in gnomad4_exome. There are 44 alleles in male gnomad4_exome subpopulation. Median coverage is 29. This position pass quality control queck.
BS2
High AC in GnomAd4 at 15 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PKD2NM_000297.4 linkc.70C>T p.Pro24Ser missense_variant Exon 1 of 15 ENST00000237596.7 NP_000288.1 Q13563-1Q9UEU6
PKD2XM_011532028.3 linkc.70C>T p.Pro24Ser missense_variant Exon 1 of 14 XP_011530330.1
PKD2NR_156488.2 linkn.169C>T non_coding_transcript_exon_variant Exon 1 of 14

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PKD2ENST00000237596.7 linkc.70C>T p.Pro24Ser missense_variant Exon 1 of 15 1 NM_000297.4 ENSP00000237596.2 Q13563-1
ENSG00000286618ENST00000662475.1 linkn.112+563G>A intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.000101
AC:
15
AN:
148720
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000243
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00380
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000150
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000841
AC:
9
AN:
10696
Hom.:
0
AF XY:
0.000628
AC XY:
4
AN XY:
6368
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00383
Gnomad ASJ exome
AF:
0.00111
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000795
AC:
81
AN:
1018634
Hom.:
0
Cov.:
29
AF XY:
0.0000905
AC XY:
44
AN XY:
486388
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00108
Gnomad4 ASJ exome
AF:
0.00440
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000182
Gnomad4 OTH exome
AF:
0.000157
GnomAD4 genome
AF:
0.000101
AC:
15
AN:
148720
Hom.:
0
Cov.:
32
AF XY:
0.0000828
AC XY:
6
AN XY:
72446
show subpopulations
Gnomad4 AFR
AF:
0.0000243
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00380
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000150
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000712
Hom.:
0
Bravo
AF:
0.000121

ClinVar

Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Autosomal dominant polycystic kidney disease Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpNov 25, 2024- -
PKD2-related disorder Benign:1
Benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesAug 23, 2022This 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.070
BayesDel_addAF
Benign
-0.51
T
BayesDel_noAF
Benign
-0.51
CADD
Benign
8.4
DANN
Uncertain
0.98
DEOGEN2
Benign
0.15
T
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.3
FATHMM_MKL
Benign
0.010
N
LIST_S2
Benign
0.45
T
M_CAP
Pathogenic
0.30
D
MetaRNN
Benign
0.0056
T
MetaSVM
Benign
-0.93
T
MutationAssessor
Benign
0.0
N
PrimateAI
Pathogenic
0.83
D
PROVEAN
Benign
-0.070
N
REVEL
Benign
0.045
Sift
Benign
1.0
T
Sift4G
Benign
0.91
T
Polyphen
0.0
B
Vest4
0.026
MutPred
0.20
Loss of relative solvent accessibility (P = 0.0071);
MVP
0.38
MPC
0.15
ClinPred
0.024
T
GERP RS
-2.4
Varity_R
0.026
gMVP
0.19

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs786204221; hg19: chr4-88928955; API