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GeneBe

7-131504383-C-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_001018111.3(PODXL):c.1605G>T(p.Gly535=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00335 in 1,614,162 control chromosomes in the GnomAD database, including 114 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.016 ( 47 hom., cov: 32)
Exomes 𝑓: 0.0020 ( 67 hom. )

Consequence

PODXL
NM_001018111.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.407
Variant links:
Genes affected
PODXL (HGNC:9171): (podocalyxin like) This gene encodes a member of the sialomucin protein family. The encoded protein was originally identified as an important component of glomerular podocytes. Podocytes are highly differentiated epithelial cells with interdigitating foot processes covering the outer aspect of the glomerular basement membrane. Other biological activities of the encoded protein include: binding in a membrane protein complex with Na+/H+ exchanger regulatory factor to intracellular cytoskeletal elements, playing a role in hematopoetic cell differentiation, and being expressed in vascular endothelium cells and binding to L-selectin. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 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=-0.31).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-131504383-C-A is Benign according to our data. Variant chr7-131504383-C-A is described in ClinVar as [Benign]. Clinvar id is 786111.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=0.407 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0517 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PODXLNM_001018111.3 linkuse as main transcriptc.1605G>T p.Gly535= synonymous_variant 9/9 ENST00000378555.8
PODXLNM_005397.4 linkuse as main transcriptc.1509G>T p.Gly503= synonymous_variant 8/8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PODXLENST00000378555.8 linkuse as main transcriptc.1605G>T p.Gly535= synonymous_variant 9/91 NM_001018111.3 P2O00592-1
PODXLENST00000322985.9 linkuse as main transcriptc.1509G>T p.Gly503= synonymous_variant 8/81 A2O00592-2
PODXLENST00000484346.1 linkuse as main transcriptn.364G>T non_coding_transcript_exon_variant 2/22
PODXLENST00000446198.5 linkuse as main transcriptc.*870G>T 3_prime_UTR_variant, NMD_transcript_variant 7/72

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0161
AC:
2455
AN:
152168
Hom.:
47
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0537
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00981
Gnomad ASJ
AF:
0.00173
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.000617
Gnomad OTH
AF:
0.0153
GnomAD3 exomes
AF:
0.00467
AC:
1174
AN:
251474
Hom.:
26
AF XY:
0.00349
AC XY:
474
AN XY:
135912
show subpopulations
Gnomad AFR exome
AF:
0.0543
Gnomad AMR exome
AF:
0.00492
Gnomad ASJ exome
AF:
0.00228
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.0000462
Gnomad NFE exome
AF:
0.000633
Gnomad OTH exome
AF:
0.00407
GnomAD4 exome
AF:
0.00202
AC:
2947
AN:
1461876
Hom.:
67
Cov.:
31
AF XY:
0.00180
AC XY:
1306
AN XY:
727242
show subpopulations
Gnomad4 AFR exome
AF:
0.0562
Gnomad4 AMR exome
AF:
0.00555
Gnomad4 ASJ exome
AF:
0.00245
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.0000936
Gnomad4 NFE exome
AF:
0.000388
Gnomad4 OTH exome
AF:
0.00460
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0161
AC:
2455
AN:
152286
Hom.:
47
Cov.:
32
AF XY:
0.0156
AC XY:
1165
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.0535
Gnomad4 AMR
AF:
0.00973
Gnomad4 ASJ
AF:
0.00173
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000617
Gnomad4 OTH
AF:
0.0151
Alfa
AF:
0.00314
Hom.:
10
Bravo
AF:
0.0183
Asia WGS
AF:
0.00231
AC:
8
AN:
3478
EpiCase
AF:
0.000273
EpiControl
AF:
0.000533

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 testingInvitaeJan 28, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.31
Cadd
Benign
6.4
Dann
Benign
0.72

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: rs34520552; hg19: chr7-131189142; API