19-726990-A-C
Position:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_002579.3(PALM):c.58-18A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0045 ( 0 hom., cov: 30)
Exomes 𝑓: 0.11 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PALM
NM_002579.3 intron
NM_002579.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.67
Genes affected
PALM (HGNC:8594): (paralemmin) This gene encodes a member of the paralemmin protein family. The product of this gene is a prenylated and palmitoylated phosphoprotein that associates with the cytoplasmic face of plasma membranes and is implicated in plasma membrane dynamics in neurons and other cell types. Several alternatively spliced transcript variants have been identified, but the full-length nature of only two transcript variants has been determined. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 19-726990-A-C is Benign according to our data. Variant chr19-726990-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 1628350.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PALM | NM_002579.3 | c.58-18A>C | intron_variant | ENST00000338448.10 | NP_002570.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 539AN: 118812Hom.: 0 Cov.: 30 FAILED QC
GnomAD3 genomes
AF:
AC:
539
AN:
118812
Hom.:
Cov.:
30
FAILED QC
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:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.105 AC: 41061AN: 391052Hom.: 0 Cov.: 8 AF XY: 0.0951 AC XY: 20027AN XY: 210506
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
41061
AN:
391052
Hom.:
Cov.:
8
AF XY:
AC XY:
20027
AN XY:
210506
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 Data not reliable, filtered out with message: AS_VQSR AF: 0.00454 AC: 540AN: 118880Hom.: 0 Cov.: 30 AF XY: 0.00461 AC XY: 264AN XY: 57240
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
540
AN:
118880
Hom.:
Cov.:
30
AF XY:
AC XY:
264
AN XY:
57240
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.:
ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 07, 2025 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
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