Genetic Variant PALM:c.5+12C>G (chr19-709163-C-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_002579.3(PALM):c.5+12C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000774 in 322,926 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 Likely benign (★).

Frequency

Genomes: 𝑓 0.000047 ( 0 hom., cov: 31)

Exomes 𝑓: 0.00010 ( 0 hom. )

Consequence

PALM
NM_002579.3 intron

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0580

Publications

0 publications found

Variant links:

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]

PALM links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 19-709163-C-G is Benign according to our data. Variant chr19-709163-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2967681.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PALM	NM_002579.3 link	c.5+12C>G		intron_variant	Intron 1 of 8	ENST00000338448.10	NP_002570.2	O75781-1A0A024R1Y6
PALM	NM_001040134.2 link	c.5+12C>G		intron_variant	Intron 1 of 7		NP_001035224.1	O75781-2A0A024R207

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PALM	ENST00000338448.10 link	c.5+12C>G	intron_variant	Intron 1 of 8	1	NM_002579.3	ENSP00000341911.4	O75781-1
PALM	ENST00000264560.11 link	c.5+12C>G	intron_variant	Intron 1 of 7	4		ENSP00000264560.7	O75781-2
PALM	ENST00000589012.5 link	n.21+12C>G	intron_variant	Intron 1 of 6	3
PALM	ENST00000592870.5 link	n.55+12C>G	intron_variant	Intron 1 of 5	2

Frequencies

GnomAD3 genomes

AF:

0.0000469

AC:

AN:

149278

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000664

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000896

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000104

AC:

AN:

173534

Hom.:

Cov.:

AF XY:

0.0000899

AC XY:

AN XY:

89016

show subpopulations

African (AFR)

AF:

0.000232

AC:

AN:

4302

American (AMR)

AF:

0.00

AC:

AN:

4894

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

5784

East Asian (EAS)

AF:

0.00

AC:

AN:

16390

South Asian (SAS)

AF:

0.00

AC:

AN:

2394

European-Finnish (FIN)

AF:

0.00

AC:

AN:

17428

Middle Eastern (MID)

AF:

0.00

AC:

AN:

868

European-Non Finnish (NFE)

AF:

0.000145

AC:

AN:

110640

Other (OTH)

AF:

0.0000923

AC:

AN:

10834

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.533

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0000469

AC:

AN:

149392

Hom.:

Cov.:

AF XY:

0.0000549

AC XY:

AN XY:

72926

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41062

American (AMR)

AF:

0.0000663

AC:

AN:

15080

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3426

East Asian (EAS)

AF:

0.00

AC:

AN:

4994

South Asian (SAS)

AF:

0.00

AC:

AN:

4792

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9842

Middle Eastern (MID)

AF:

0.00

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.0000896

AC:

AN:

66936

Other (OTH)

AF:

0.00

AC:

AN:

2066

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.596

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.000142

Hom.:

Bravo

AF:

0.0000604

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jul 19, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

8.2

(source)

DANN

Benign

0.87

PhyloP100

0.058

PromoterAI

-0.11

Neutral

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

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

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19-709163-C-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over