rs1327796

Variant names:

• chr9-109764009-C-G
• rs1327796
• ENST00000374531.6:c.6-16479C>G

Your query was ambiguous. Multiple possible variants found:

• chr9-109764009-C-G
• chr9-109764009-C-T

Variant summary

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

The ENST00000374531.6(PALM2AKAP2):​c.6-16479C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,054 control chromosomes in the GnomAD database, including 3,075 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 0.20 (3075 hom., cov: 32)
• Consequence: PALM2AKAP2 ENST00000374531.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 11 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]

ENSG00000232939 (HGNC:58228):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PALM2AKAP2	NM_001037293.3	c.6-16479C>G		intron_variant	Intron 1 of 6		NP_001032370.1
PALM2AKAP2-AS1	NR_171891.1	n.445+1404G>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PALM2AKAP2	ENST00000374531.6	c.6-16479C>G		intron_variant	Intron 1 of 6	1		ENSP00000363656.2
PALM2AKAP2	ENST00000674068.1	c.-1-16479C>G		intron_variant	Intron 2 of 2			ENSP00000501308.1
ENSG00000232939	ENST00000449258.4	n.517+1404G>C		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29922 AN: 151936 Hom.: 3070 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.197 AC: 29952 AN: 152054 Hom.: 3075 Cov.: 32 AF XY: 0.199 AC XY: 14802 AN XY: 74330

African (AFR) AF: 0.216 AC: 8936 AN: 41434

American (AMR) AF: 0.211 AC: 3227 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 637 AN: 3464

East Asian (EAS) AF: 0.257 AC: 1332 AN: 5178

South Asian (SAS) AF: 0.209 AC: 1009 AN: 4822

European-Finnish (FIN) AF: 0.219 AC: 2316 AN: 10580

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11894 AN: 67974

Other (OTH) AF: 0.180 AC: 380 AN: 2114

Alfa AF: 0.182 Hom.: 1417

Bravo AF: 0.197

Asia WGS AF: 0.254 AC: 882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.4
DANN	Benign	0.60
PhyloP100		0.33
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: rs1327796; hg19: chr9-112526289; COSMIC: COSV65759149;