19-726999-T-A

Variant names:

• chr19-726999-T-A
• rs1210670058
• NM_002579.3:c.58-9T>A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_002579.3(PALM):​c.58-9T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00028 (0 hom., cov: 25)
  • Exomes 𝑓: 0.0063 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PALM NM_002579.3 intron
• Scores: Splicing: ADA: 0.004078
• Clinical Significance: Not reported in ClinVar
• 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 -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PALM	NM_002579.3	c.58-9T>A		intron_variant	Intron 2 of 8	ENST00000338448.10	NP_002570.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PALM	ENST00000338448.10	c.58-9T>A		intron_variant	Intron 2 of 8	1	NM_002579.3	ENSP00000341911.4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 23 AN: 82900 Hom.: 0 Cov.: 25 FAILED QC

Gnomad AFR AF: 0.0000464

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000286

Gnomad ASJ AF: 0.000460

Gnomad EAS AF: 0.000333

Gnomad SAS AF: 0.000397

Gnomad FIN AF: 0.000545

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000315

Gnomad OTH AF: 0.00189

GnomAD4 exome AF: 0.00626 AC: 2341 AN: 374022 Hom.: 0 Cov.: 11 AF XY: 0.00586 AC XY: 1162 AN XY: 198130

Gnomad4 AFR exome AF: 0.00530

Gnomad4 AMR exome AF: 0.00155

Gnomad4 ASJ exome AF: 0.00427

Gnomad4 EAS exome AF: 0.00828

Gnomad4 SAS exome AF: 0.000902

Gnomad4 FIN exome AF: 0.000878

Gnomad4 NFE exome AF: 0.00815

Gnomad4 OTH exome AF: 0.00639

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000277 AC: 23 AN: 82962 Hom.: 0 Cov.: 25 AF XY: 0.000325 AC XY: 13 AN XY: 39940

Gnomad4 AFR AF: 0.0000464

Gnomad4 AMR AF: 0.000286

Gnomad4 ASJ AF: 0.000460

Gnomad4 EAS AF: 0.000332

Gnomad4 SAS AF: 0.000396

Gnomad4 FIN AF: 0.000545

Gnomad4 NFE AF: 0.000315

Gnomad4 OTH AF: 0.00187

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	7.0
DANN	Benign	0.67
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.0041
dbscSNV1_RF	Benign	0.13
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;