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GeneBe

10-100294640-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_016112.3(PKD2L1):c.1554G>A(p.Arg518=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00196 in 1,614,116 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0017 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0020 ( 18 hom. )

Consequence

PKD2L1
NM_016112.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.309
Variant links:
Genes affected
PKD2L1 (HGNC:9011): (polycystin 2 like 1, transient receptor potential cation channel) This gene encodes a member of the polycystin protein family. The encoded protein contains multiple transmembrane domains, and cytoplasmic N- and C-termini. The protein may be an integral membrane protein involved in cell-cell/matrix interactions. This protein functions as a calcium-regulated nonselective cation channel. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 10-100294640-C-T is Benign according to our data. Variant chr10-100294640-C-T is described in ClinVar as [Benign]. Clinvar id is 712587.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.309 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 256 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PKD2L1NM_016112.3 linkuse as main transcriptc.1554G>A p.Arg518= synonymous_variant 9/16 ENST00000318222.4
PKD2L1NM_001253837.2 linkuse as main transcriptc.1413G>A p.Arg471= synonymous_variant 9/16

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PKD2L1ENST00000318222.4 linkuse as main transcriptc.1554G>A p.Arg518= synonymous_variant 9/161 NM_016112.3 P1Q9P0L9-1
PKD2L1ENST00000528248.1 linkuse as main transcriptc.*1294G>A 3_prime_UTR_variant, NMD_transcript_variant 9/161
PKD2L1ENST00000465680.2 linkuse as main transcriptc.105-6162G>A intron_variant 3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00168
AC:
256
AN:
152132
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000290
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00242
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0112
Gnomad FIN
AF:
0.000566
Gnomad MID
AF:
0.0285
Gnomad NFE
AF:
0.00193
Gnomad OTH
AF:
0.00288
GnomAD3 exomes
AF:
0.00303
AC:
763
AN:
251488
Hom.:
7
AF XY:
0.00369
AC XY:
502
AN XY:
135918
show subpopulations
Gnomad AFR exome
AF:
0.000369
Gnomad AMR exome
AF:
0.00231
Gnomad ASJ exome
AF:
0.000595
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0113
Gnomad FIN exome
AF:
0.000416
Gnomad NFE exome
AF:
0.00251
Gnomad OTH exome
AF:
0.00521
GnomAD4 exome
AF:
0.00199
AC:
2911
AN:
1461866
Hom.:
18
Cov.:
32
AF XY:
0.00238
AC XY:
1733
AN XY:
727234
show subpopulations
Gnomad4 AFR exome
AF:
0.000209
Gnomad4 AMR exome
AF:
0.00221
Gnomad4 ASJ exome
AF:
0.000191
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0116
Gnomad4 FIN exome
AF:
0.000374
Gnomad4 NFE exome
AF:
0.00140
Gnomad4 OTH exome
AF:
0.00272
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00168
AC:
256
AN:
152250
Hom.:
0
Cov.:
31
AF XY:
0.00192
AC XY:
143
AN XY:
74424
show subpopulations
Gnomad4 AFR
AF:
0.000289
Gnomad4 AMR
AF:
0.00242
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0112
Gnomad4 FIN
AF:
0.000566
Gnomad4 NFE
AF:
0.00193
Gnomad4 OTH
AF:
0.00285
Alfa
AF:
0.00152
Hom.:
0
Bravo
AF:
0.00160
Asia WGS
AF:
0.00404
AC:
14
AN:
3478
EpiCase
AF:
0.00398
EpiControl
AF:
0.00338

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeFeb 27, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.33
Cadd
Benign
11
Dann
Benign
0.64

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: rs141868275; hg19: chr10-102054397; API