rs9459160

Variant names:

• chr6-158023427-G-A
• rs9459160
• NM_003898.4:c.215-5329G>A

Variant summary

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

The NM_003898.4(SYNJ2):​c.215-5329G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,030 control chromosomes in the GnomAD database, including 3,406 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 0.16 (3406 hom., cov: 31)
• Consequence: SYNJ2 NM_003898.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812
• Publications: 2 publications found

Genes affected

SYNJ2 (HGNC:11504): (synaptojanin 2) The gene is a member of the inositol-polyphosphate 5-phosphatase family. The encoded protein interacts with the ras-related C3 botulinum toxin substrate 1, which causes translocation of the encoded protein to the plasma membrane where it inhibits clathrin-mediated endocytosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

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 (AFR) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003898.4. 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
	SYNJ2	NM_003898.4	MANE Select	c.215-5329G>A		intron	N/A	NP_003889.1	O15056-1
	SYNJ2	NM_001410947.1		c.215-5329G>A		intron	N/A	NP_001397876.1	O15056-3
	SYNJ2	NM_001178088.2		c.-497-5329G>A		intron	N/A	NP_001171559.1	A0A1W2PR85

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYNJ2	ENST00000355585.9	TSL:1 MANE Select	c.215-5329G>A		intron	N/A	ENSP00000347792.4	O15056-1
	SYNJ2	ENST00000640338.1	TSL:1	c.215-5329G>A		intron	N/A	ENSP00000492532.1	O15056-3
	SYNJ2	ENST00000638626.1	TSL:1	c.-497-5329G>A		intron	N/A	ENSP00000492369.1	A0A1W2PR85

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24980 AN: 151912 Hom.: 3392 Cov.: 31

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0999

Gnomad ASJ AF: 0.0749

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0793

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.165 AC: 25022 AN: 152030 Hom.: 3406 Cov.: 31 AF XY: 0.161 AC XY: 11955 AN XY: 74334

African (AFR) AF: 0.371 AC: 15372 AN: 41406

American (AMR) AF: 0.0998 AC: 1525 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0749 AC: 260 AN: 3472

East Asian (EAS) AF: 0.129 AC: 668 AN: 5168

South Asian (SAS) AF: 0.193 AC: 929 AN: 4816

European-Finnish (FIN) AF: 0.0521 AC: 552 AN: 10592

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0792 AC: 5386 AN: 67972

Other (OTH) AF: 0.141 AC: 298 AN: 2110

Alfa AF: 0.117 Hom.: 2505

Bravo AF: 0.175

Asia WGS AF: 0.186 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.60
PhyloP100		-0.81
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: rs9459160; hg19: chr6-158444459;