9-110129355-C-T

Position:

• chr9-110129355-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007203.5(PALM2AKAP2):​c.583-6772C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0704 in 152,284 control chromosomes in the GnomAD database, including 566 homozygotes. 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 0.070 (566 hom., cov: 33)
• Consequence: PALM2AKAP2 NM_007203.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PALM2AKAP2	NM_007203.5	c.583-6772C>T		intron_variant		ENST00000374530.8	NP_009134.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PALM2AKAP2	ENST00000374530.8	c.583-6772C>T		intron_variant		2	NM_007203.5	ENSP00000363654.3

Frequencies

GnomAD3 genomes AF: 0.0703 AC: 10703 AN: 152166 Hom.: 561 Cov.: 33

Gnomad AFR AF: 0.0168

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.0978

Gnomad FIN AF: 0.0843

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0780

Gnomad OTH AF: 0.0788

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0704 AC: 10717 AN: 152284 Hom.: 566 Cov.: 33 AF XY: 0.0741 AC XY: 5518 AN XY: 74472

Gnomad4 AFR AF: 0.0167

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.0271

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.0974

Gnomad4 FIN AF: 0.0843

Gnomad4 NFE AF: 0.0780

Gnomad4 OTH AF: 0.0822

Alfa AF: 0.0825 Hom.: 104

Bravo AF: 0.0725

Asia WGS AF: 0.165 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
DANN	Benign	0.52

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

LitVar

Other links and lift over

dbSNP: rs17806457; hg19: chr9-112891635;