rs13217929

Variant names:

• chr6-158094079-C-A
• rs13217929
• ENST00000640338.1:c.*69C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-158094079-C-A
• chr6-158094079-C-G
• chr6-158094079-C-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000640338.1(SYNJ2):​c.*69C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000829 in 723,768 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00022 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000045 (0 hom.)
• Consequence: SYNJ2 ENST00000640338.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468
• 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SYNJ2	NM_003898.4	c.3744+975C>A		intron_variant	Intron 26 of 26	ENST00000355585.9	NP_003889.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SYNJ2	ENST00000355585.9	c.3744+975C>A		intron_variant	Intron 26 of 26	1	NM_003898.4	ENSP00000347792.4

Frequencies

GnomAD3 genomes AF: 0.000224 AC: 34 AN: 151964 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000725

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.000962

GnomAD4 exome AF: 0.0000455 AC: 26 AN: 571686 Hom.: 0 Cov.: 0 AF XY: 0.0000355 AC XY: 11 AN XY: 309522

African (AFR) AF: 0.00122 AC: 20 AN: 16356

American (AMR) AF: 0.00 AC: 0 AN: 39084

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19504

East Asian (EAS) AF: 0.0000286 AC: 1 AN: 34930

South Asian (SAS) AF: 0.00 AC: 0 AN: 63706

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 36794

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3604

European-Non Finnish (NFE) AF: 0.0000122 AC: 4 AN: 326594

Other (OTH) AF: 0.0000321 AC: 1 AN: 31114

GnomAD4 genome AF: 0.000224 AC: 34 AN: 152082 Hom.: 0 Cov.: 31 AF XY: 0.000256 AC XY: 19 AN XY: 74342

African (AFR) AF: 0.000723 AC: 30 AN: 41492

American (AMR) AF: 0.00 AC: 0 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5170

South Asian (SAS) AF: 0.00 AC: 0 AN: 4808

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10580

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67976

Other (OTH) AF: 0.000952 AC: 2 AN: 2100

Alfa AF: 0.00 Hom.: 2183

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.1
DANN	Benign	0.60
PhyloP100		-0.47

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: rs13217929; hg19: chr6-158515111;