ENST00000674068.1:c.-2+111568A>G

Variant names:

• chr9-109626179-A-G
• rs1407392
• ENST00000674068.1:c.-2+111568A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000674068.1(PALM2AKAP2):​c.-2+111568A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,990 control chromosomes in the GnomAD database, including 14,411 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 0.43 (14411 hom., cov: 32)
• Consequence: PALM2AKAP2 ENST00000674068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000674068.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PALM2AKAP2	ENST00000674068.1		c.-2+111568A>G		intron	N/A	ENSP00000501308.1	A0A669KBK1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65110 AN: 151872 Hom.: 14392 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.429 AC: 65170 AN: 151990 Hom.: 14411 Cov.: 32 AF XY: 0.422 AC XY: 31311 AN XY: 74270

African (AFR) AF: 0.421 AC: 17451 AN: 41446

American (AMR) AF: 0.342 AC: 5221 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1594 AN: 3472

East Asian (EAS) AF: 0.143 AC: 737 AN: 5170

South Asian (SAS) AF: 0.433 AC: 2088 AN: 4822

European-Finnish (FIN) AF: 0.417 AC: 4399 AN: 10552

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32101 AN: 67954

Other (OTH) AF: 0.429 AC: 905 AN: 2108

Alfa AF: 0.436 Hom.: 2176

Bravo AF: 0.418

Asia WGS AF: 0.343 AC: 1192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.1
DANN	Benign	0.56
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs1407392; hg19: chr9-112388459;