rs738536

Variant names:

• chr22-42864421-G-A
• rs738536
• ENST00000507586.1:n.71-5899C>T

Variant summary

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

The ENST00000507586.1(PACSIN2):​n.71-5899C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 152,014 control chromosomes in the GnomAD database, including 14,799 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 (14799 hom., cov: 32)
• Consequence: PACSIN2 ENST00000507586.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 14 publications found

Genes affected

PACSIN2 (HGNC:8571): (protein kinase C and casein kinase substrate in neurons 2) This gene is a member of the protein kinase C and casein kinase substrate in neurons family. The encoded protein is involved in linking the actin cytoskeleton with vesicle formation by regulating tubulin polymerization. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

ENSG00000307798 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507586.1. 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
	PACSIN2	ENST00000507586.1	TSL:3	n.71-5899C>T		intron	N/A	ENSP00000422788.1	H0Y923
	ENSG00000307798	ENST00000828835.1		n.197-6854G>A		intron	N/A
	ENSG00000307798	ENST00000828836.1		n.159-6810G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65795 AN: 151896 Hom.: 14778 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.0954

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.433 AC: 65845 AN: 152014 Hom.: 14799 Cov.: 32 AF XY: 0.427 AC XY: 31709 AN XY: 74292

African (AFR) AF: 0.414 AC: 17175 AN: 41438

American (AMR) AF: 0.424 AC: 6476 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1483 AN: 3472

East Asian (EAS) AF: 0.0947 AC: 490 AN: 5176

South Asian (SAS) AF: 0.416 AC: 2006 AN: 4820

European-Finnish (FIN) AF: 0.361 AC: 3799 AN: 10538

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32903 AN: 67978

Other (OTH) AF: 0.442 AC: 933 AN: 2110

Alfa AF: 0.468 Hom.: 22966

Bravo AF: 0.432

Asia WGS AF: 0.275 AC: 959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.31
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs738536; hg19: chr22-43260427;