Variant 9-110048735-TCCCCCGGAGTCTCCTGGA-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM4BP6_Very_StrongBA1

The ENST00000434623.6(PALM2AKAP2):c.64_81del(p.Ser22_Glu27del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0564 in 1,538,218 control chromosomes in the GnomAD database, including 2,885 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.042 ( 199 hom., cov: 30)

Exomes 𝑓: 0.058 ( 2686 hom. )

Consequence

PALM2AKAP2
ENST00000434623.6 inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.910

Variant links:

Genes affected

PALM2AKAP2 (HGNC:33529): (PALM2 and AKAP2 fusion) This gene belongs to the paralemmin downstream gene (PDG) family defined in PMID:22855693. Paralemmin downstream genes may have evolved contiguously with the paralemmin genes and are associated with other paralemmin paralogs in humans and several other taxa. The gene encodes three distinct protein isoforms, the PALM2 isoform, the AKAP2 isoform and the PALM2-AKAP2 isoform. The biological significance of the PALM2-AKAP2 isoforms is yet unknown. Earlier, PALM2 and AKAP2 were annotated as separate genes and PALM2-AKAP2 was annotated as a readthrough gene. [provided by RefSeq, May 2019]

PALM2AKAP2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in ENST00000434623.6.

BP6

Variant 9-110048735-TCCCCCGGAGTCTCCTGGA-T is Benign according to our data. Variant chr9-110048735-TCCCCCGGAGTCTCCTGGA-T is described in ClinVar as [Benign]. Clinvar id is 252563.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PALM2AKAP2	NM_007203.5 linkuse as main transcript	c.582+32724_582+32741del		intron_variant		ENST00000374530.8	NP_009134.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PALM2AKAP2	ENST00000374530.8 linkuse as main transcript	c.582+32724_582+32741del		intron_variant		2	NM_007203.5	ENSP00000363654

Frequencies

GnomAD3 genomes

AF:

0.0422

AC:

6381

AN:

151304

Hom.:

200

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0124

Gnomad AMI

AF:

0.0176

Gnomad AMR

AF:

0.0376

Gnomad ASJ

AF:

0.0791

Gnomad EAS

AF:

0.0516

Gnomad SAS

AF:

0.110

Gnomad FIN

AF:

0.0148

Gnomad MID

AF:

0.0609

Gnomad NFE

AF:

0.0584

Gnomad OTH

AF:

0.0453

GnomAD3 exomes

AF:

0.0395

AC:

5557

AN:

140564

Hom.:

263

AF XY:

0.0426

AC XY:

3333

AN XY:

78148

show subpopulations

Gnomad AFR exome

AF:

0.00448

Gnomad AMR exome

AF:

0.0200

Gnomad ASJ exome

AF:

0.0583

Gnomad EAS exome

AF:

0.0343

Gnomad SAS exome

AF:

0.0790

Gnomad FIN exome

AF:

0.0106

Gnomad NFE exome

AF:

0.0380

Gnomad OTH exome

AF:

0.0487

GnomAD4 exome

AF:

0.0580

AC:

80433

AN:

1386798

Hom.:

2686

AF XY:

0.0597

AC XY:

40963

AN XY:

686136

show subpopulations

Gnomad4 AFR exome

AF:

0.00922

Gnomad4 AMR exome

AF:

0.0279

Gnomad4 ASJ exome

AF:

0.0719

Gnomad4 EAS exome

AF:

0.0527

Gnomad4 SAS exome

AF:

0.0982

Gnomad4 FIN exome

AF:

0.0228

Gnomad4 NFE exome

AF:

0.0584

Gnomad4 OTH exome

AF:

0.0573

GnomAD4 genome

AF:

0.0421

AC:

6371

AN:

151420

Hom.:

199

Cov.:

AF XY:

0.0408

AC XY:

3020

AN XY:

74030

show subpopulations

Gnomad4 AFR

AF:

0.0124

Gnomad4 AMR

AF:

0.0374

Gnomad4 ASJ

AF:

0.0791

Gnomad4 EAS

AF:

0.0510

Gnomad4 SAS

AF:

0.109

Gnomad4 FIN

AF:

0.0148

Gnomad4 NFE

AF:

0.0584

Gnomad4 OTH

AF:

0.0448

Alfa

AF:

0.0221

Hom.:

Bravo

AF:

0.0405

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia

Nov 24, 2015

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over