rs1744169

Variant names:

• chr6-158087193-A-G
• rs1744169
• NM_003898.4:c.3343+204A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-158087193-A-G
• chr6-158087193-A-T

Variant summary

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

The NM_003898.4(SYNJ2):​c.3343+204A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 152,096 control chromosomes in the GnomAD database, including 36,600 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 0.68 (36600 hom., cov: 32)
• Consequence: SYNJ2 NM_003898.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 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.3343+204A>G		intron	N/A	NP_003889.1	O15056-1
	SYNJ2	NM_001410947.1		c.3343+204A>G		intron	N/A	NP_001397876.1	O15056-3
	SYNJ2	NM_001178088.2		c.2632+204A>G		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.3343+204A>G		intron	N/A	ENSP00000347792.4	O15056-1
	SYNJ2	ENST00000640338.1	TSL:1	c.3343+204A>G		intron	N/A	ENSP00000492532.1	O15056-3
	SYNJ2	ENST00000638626.1	TSL:1	c.2632+204A>G		intron	N/A	ENSP00000492369.1	A0A1W2PR85

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103371 AN: 151980 Hom.: 36555 Cov.: 32

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.680 AC: 103458 AN: 152096 Hom.: 36600 Cov.: 32 AF XY: 0.676 AC XY: 50254 AN XY: 74326

African (AFR) AF: 0.889 AC: 36921 AN: 41522

American (AMR) AF: 0.466 AC: 7122 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2006 AN: 3470

East Asian (EAS) AF: 0.592 AC: 3054 AN: 5158

South Asian (SAS) AF: 0.618 AC: 2972 AN: 4808

European-Finnish (FIN) AF: 0.646 AC: 6823 AN: 10564

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42394 AN: 67978

Other (OTH) AF: 0.637 AC: 1348 AN: 2116

Alfa AF: 0.632 Hom.: 15611

Bravo AF: 0.673

Asia WGS AF: 0.624 AC: 2173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.89
DANN	Benign	0.19
PhyloP100		-1.3
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: rs1744169; hg19: chr6-158508225; COSMIC: COSV62900391;