chr7-131504335-A-G
Position:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001018111.3(PODXL):āc.1653T>Cā(p.Asp551=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000458 in 1,613,974 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.000085 ( 0 hom., cov: 32)
Exomes š: 0.000042 ( 0 hom. )
Consequence
PODXL
NM_001018111.3 synonymous
NM_001018111.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.08
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 Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 7-131504335-A-G is Benign according to our data. Variant chr7-131504335-A-G is described in ClinVar as [Benign]. Clinvar id is 1555206.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.09 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PODXL | NM_001018111.3 | c.1653T>C | p.Asp551= | synonymous_variant | 9/9 | ENST00000378555.8 | |
PODXL | NM_005397.4 | c.1557T>C | p.Asp519= | synonymous_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PODXL | ENST00000378555.8 | c.1653T>C | p.Asp551= | synonymous_variant | 9/9 | 1 | NM_001018111.3 | P2 | |
PODXL | ENST00000322985.9 | c.1557T>C | p.Asp519= | synonymous_variant | 8/8 | 1 | A2 | ||
PODXL | ENST00000484346.1 | n.412T>C | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
PODXL | ENST00000446198.5 | c.*918T>C | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152094Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
13
AN:
152094
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0000875 AC: 22AN: 251404Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135882
GnomAD3 exomes
AF:
AC:
22
AN:
251404
Hom.:
AF XY:
AC XY:
16
AN XY:
135882
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000417 AC: 61AN: 1461880Hom.: 0 Cov.: 31 AF XY: 0.0000440 AC XY: 32AN XY: 727238
GnomAD4 exome
AF:
AC:
61
AN:
1461880
Hom.:
Cov.:
31
AF XY:
AC XY:
32
AN XY:
727238
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000855 AC: 13AN: 152094Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74280
GnomAD4 genome
AF:
AC:
13
AN:
152094
Hom.:
Cov.:
32
AF XY:
AC XY:
3
AN XY:
74280
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1
AN:
3478
EpiCase
AF:
EpiControl
AF:
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 submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 20, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at