rs7038399

chr9-110091231-G-Achr9-110091231-G-T

Variant summary

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

The NM_007203.5(PALM2AKAP2):c.583-44896G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,066 control chromosomes in the GnomAD database, including 1,028 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 0.10 (1028 hom., cov: 31)
• Consequence: PALM2AKAP2 NM_007203.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PALM2AKAP2	NM_007203.5	c.583-44896G>A		intron_variant		ENST00000374530.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PALM2AKAP2	ENST00000374530.8	c.583-44896G>A		intron_variant		2	NM_007203.5

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15256 AN: 151948 Hom.: 1016 Cov.: 31

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.0685

Gnomad ASJ AF: 0.0551

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0543

Gnomad FIN AF: 0.0321

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0783

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.101 AC: 15301 AN: 152066 Hom.: 1028 Cov.: 31 AF XY: 0.0966 AC XY: 7183 AN XY: 74334

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.0684

Gnomad4 ASJ AF: 0.0551

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0542

Gnomad4 FIN AF: 0.0321

Gnomad4 NFE AF: 0.0783

Gnomad4 OTH AF: 0.0999

Alfa AF: 0.0780 Hom.: 556

Bravo AF: 0.107

Asia WGS AF: 0.0440 AC: 152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.11
Dann	Benign	0.68

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: rs7038399; hg19: chr9-112853511;