rs7364152

Positions:

• chr22-42920661-A-G
• chr22-42920661-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000263246.8(PACSIN2):​c.-77-8504T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 151,952 control chromosomes in the GnomAD database, including 36,707 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 0.67 (36707 hom., cov: 30)
• Consequence: PACSIN2 ENST00000263246.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PACSIN2	NM_001184970.3	c.-77-8504T>C		intron_variant		ENST00000263246.8	NP_001171899.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PACSIN2	ENST00000263246.8	c.-77-8504T>C		intron_variant		1	NM_001184970.3	ENSP00000263246	A1

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102138 AN: 151834 Hom.: 36664 Cov.: 30

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.673 AC: 102234 AN: 151952 Hom.: 36707 Cov.: 30 AF XY: 0.672 AC XY: 49910 AN XY: 74252

Gnomad4 AFR AF: 0.916

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.821

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.663

Alfa AF: 0.617 Hom.: 5170

Bravo AF: 0.706

Asia WGS AF: 0.719 AC: 2502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.20
DANN	Benign	0.57

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

Publications

LitVar

Other links and lift over

dbSNP: rs7364152; hg19: chr22-43316667;