19-726999-T-C

Position:

• chr19-726999-T-C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_002579.3(PALM):​c.58-9T>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 0.0031 (0 hom., cov: 25)
  • Exomes 𝑓: 0.051 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PALM NM_002579.3 intron
• Scores: Splicing: ADA: 0.00002592
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.267

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]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BP6: Variant 19-726999-T-C is Benign according to our data. Variant chr19-726999-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2807193.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PALM	NM_002579.3	c.58-9T>C		intron_variant		ENST00000338448.10	NP_002570.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PALM	ENST00000338448.10	c.58-9T>C		intron_variant		1	NM_002579.3	ENSP00000341911.4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 253 AN: 82148 Hom.: 0 Cov.: 25 FAILED QC

Gnomad AFR AF: 0.00295

Gnomad AMI AF: 0.00183

Gnomad AMR AF: 0.00631

Gnomad ASJ AF: 0.00185

Gnomad EAS AF: 0.00304

Gnomad SAS AF: 0.00241

Gnomad FIN AF: 0.00864

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00214

Gnomad OTH AF: 0.00768

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0510 AC: 17158 AN: 336446 Hom.: 0 Cov.: 11 AF XY: 0.0499 AC XY: 8958 AN XY: 179424

Gnomad4 AFR exome AF: 0.0322

Gnomad4 AMR exome AF: 0.0491

Gnomad4 ASJ exome AF: 0.0407

Gnomad4 EAS exome AF: 0.0405

Gnomad4 SAS exome AF: 0.0588

Gnomad4 FIN exome AF: 0.0366

Gnomad4 NFE exome AF: 0.0526

Gnomad4 OTH exome AF: 0.0592

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00308 AC: 253 AN: 82202 Hom.: 0 Cov.: 25 AF XY: 0.00311 AC XY: 123 AN XY: 39534

Gnomad4 AFR AF: 0.00295

Gnomad4 AMR AF: 0.00630

Gnomad4 ASJ AF: 0.00185

Gnomad4 EAS AF: 0.00304

Gnomad4 SAS AF: 0.00281

Gnomad4 FIN AF: 0.00864

Gnomad4 NFE AF: 0.00212

Gnomad4 OTH AF: 0.00762

Alfa AF: 0.0379 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Apr 25, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.7
DANN	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000026
dbscSNV1_RF	Benign	0.0
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

Other links and lift over

dbSNP: rs1210670058; hg19: chr19-726999;