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GeneBe

rs2413739

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001184970.3(PACSIN2):c.-78+13991G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 152,034 control chromosomes in the GnomAD database, including 14,360 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 ( 14360 hom., cov: 32)

Consequence

PACSIN2
NM_001184970.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0540
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PACSIN2NM_001184970.3 linkuse as main transcriptc.-78+13991G>A intron_variant ENST00000263246.8
PACSIN2NM_001349969.2 linkuse as main transcriptc.-78+13991G>A intron_variant
PACSIN2NM_001349971.2 linkuse as main transcriptc.-78+13991G>A intron_variant
PACSIN2NM_001349974.2 linkuse as main transcriptc.-64+13991G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PACSIN2ENST00000263246.8 linkuse as main transcriptc.-78+13991G>A intron_variant 1 NM_001184970.3 A1Q9UNF0-1
PACSIN2ENST00000422336.5 linkuse as main transcriptc.-78+1280G>A intron_variant 5
PACSIN2ENST00000453643.5 linkuse as main transcriptc.-238-7250G>A intron_variant 5
PACSIN2ENST00000445706.5 linkuse as main transcriptn.78+13991G>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.426
AC:
64766
AN:
151916
Hom.:
14328
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.487
Gnomad AMI
AF:
0.479
Gnomad AMR
AF:
0.389
Gnomad ASJ
AF:
0.369
Gnomad EAS
AF:
0.0755
Gnomad SAS
AF:
0.403
Gnomad FIN
AF:
0.350
Gnomad MID
AF:
0.421
Gnomad NFE
AF:
0.440
Gnomad OTH
AF:
0.429
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.427
AC:
64844
AN:
152034
Hom.:
14360
Cov.:
32
AF XY:
0.420
AC XY:
31235
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.488
Gnomad4 AMR
AF:
0.389
Gnomad4 ASJ
AF:
0.369
Gnomad4 EAS
AF:
0.0751
Gnomad4 SAS
AF:
0.403
Gnomad4 FIN
AF:
0.350
Gnomad4 NFE
AF:
0.440
Gnomad4 OTH
AF:
0.423
Alfa
AF:
0.434
Hom.:
3657
Bravo
AF:
0.427
Asia WGS
AF:
0.290
AC:
1012
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
Cadd
Benign
1.0
Dann
Benign
0.67

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2413739; hg19: chr22-43397036; COSMIC: COSV54322613; API