9-110091231-G-A

Variant names:

• chr9-110091231-G-A
• rs7038399
• NM_007203.5:c.583-44896G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007203.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PALM2AKAP2	NM_007203.5	MANE Select	c.583-44896G>A		intron	N/A	NP_009134.1
	PALM2AKAP2	NM_147150.3		c.583-44896G>A		intron	N/A	NP_671492.1
	PALM2AKAP2	NM_001198656.1		c.156+42376G>A		intron	N/A	NP_001185585.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PALM2AKAP2	ENST00000374530.8	TSL:2 MANE Select	c.583-44896G>A		intron	N/A	ENSP00000363654.3
	PALM2AKAP2	ENST00000434623.6	TSL:1	c.156+42376G>A		intron	N/A	ENSP00000404782.2
	PALM2AKAP2	ENST00000374525.5	TSL:1	c.156+42376G>A		intron	N/A	ENSP00000363649.1

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

African (AFR) AF: 0.186 AC: 7701 AN: 41418

American (AMR) AF: 0.0684 AC: 1046 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0551 AC: 191 AN: 3464

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5172

South Asian (SAS) AF: 0.0542 AC: 261 AN: 4818

European-Finnish (FIN) AF: 0.0321 AC: 340 AN: 10590

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0783 AC: 5324 AN: 67994

Other (OTH) AF: 0.0999 AC: 211 AN: 2112

Alfa AF: 0.0827 Hom.: 833

Bravo AF: 0.107

Asia WGS AF: 0.0440 AC: 152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.68
PhyloP100		-0.54
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7038399; hg19: chr9-112853511;