rs17806457

Variant names:

• chr9-110129355-C-T
• rs17806457
• NM_007203.5:c.583-6772C>T

Variant summary

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

The NM_007203.5(PALM2AKAP2):​c.583-6772C>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
• Publications: 7 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 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.583-6772C>T		intron	N/A	NP_009134.1
	PALM2AKAP2	NM_147150.3		c.583-6772C>T		intron	N/A	NP_671492.1
	PALM2AKAP2	NM_001198656.1		c.157-6772C>T		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.583-6772C>T		intron	N/A	ENSP00000363654.3
	PALM2AKAP2	ENST00000434623.6	TSL:1	c.157-6772C>T		intron	N/A	ENSP00000404782.2
	PALM2AKAP2	ENST00000374525.5	TSL:1	c.157-6772C>T		intron	N/A	ENSP00000363649.1

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

African (AFR) AF: 0.0167 AC: 695 AN: 41548

American (AMR) AF: 0.134 AC: 2045 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0271 AC: 94 AN: 3468

East Asian (EAS) AF: 0.195 AC: 1015 AN: 5196

South Asian (SAS) AF: 0.0974 AC: 470 AN: 4824

European-Finnish (FIN) AF: 0.0843 AC: 895 AN: 10618

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0780 AC: 5305 AN: 68008

Other (OTH) AF: 0.0822 AC: 174 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
DANN	Benign	0.52
PhyloP100		-0.19
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: rs17806457; hg19: chr9-112891635;