chr19-726994-G-C

Position:

• chr19-726994-G-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.58-14G>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 0.0037 (0 hom., cov: 29)
  • Exomes 𝑓: 0.10 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PALM NM_002579.3 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.838

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=-0.92).
• BP6: Variant 19-726994-G-C is Benign according to our data. Variant chr19-726994-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 1631069.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.58-14G>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.58-14G>C		intron_variant		1	NM_002579.3	ENSP00000341911.4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 391 AN: 107426 Hom.: 0 Cov.: 29 FAILED QC

Gnomad AFR AF: 0.00222

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00670

Gnomad ASJ AF: 0.00214

Gnomad EAS AF: 0.00477

Gnomad SAS AF: 0.00351

Gnomad FIN AF: 0.00711

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00342

Gnomad OTH AF: 0.00808

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.101 AC: 33968 AN: 336916 Hom.: 0 Cov.: 8 AF XY: 0.0936 AC XY: 16930 AN XY: 180796

Gnomad4 AFR exome AF: 0.0758

Gnomad4 AMR exome AF: 0.0923

Gnomad4 ASJ exome AF: 0.0653

Gnomad4 EAS exome AF: 0.0864

Gnomad4 SAS exome AF: 0.0552

Gnomad4 FIN exome AF: 0.0402

Gnomad4 NFE exome AF: 0.121

Gnomad4 OTH exome AF: 0.108

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00366 AC: 393 AN: 107486 Hom.: 0 Cov.: 29 AF XY: 0.00399 AC XY: 207 AN XY: 51886

Gnomad4 AFR AF: 0.00226

Gnomad4 AMR AF: 0.00669

Gnomad4 ASJ AF: 0.00214

Gnomad4 EAS AF: 0.00507

Gnomad4 SAS AF: 0.00382

Gnomad4 FIN AF: 0.00711

Gnomad4 NFE AF: 0.00340

Gnomad4 OTH AF: 0.00803

Alfa AF: 0.00780 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

Jan 07, 2025

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.41
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs1342223766; hg19: chr19-726994;