rs7279487

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_203446.3(SYNJ1):​c.*2291A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,706 control chromosomes in the GnomAD database, including 1,290 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 0.13 ( 1287 hom., cov: 33)
Exomes 𝑓: 0.12 ( 3 hom. )

Consequence

SYNJ1
NM_203446.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.896
Variant links:
Genes affected
SYNJ1 (HGNC:11503): (synaptojanin 1) This gene encodes a phosphoinositide phosphatase that regulates levels of membrane phosphatidylinositol-4,5-bisphosphate. As such, expression of this enzyme may affect synaptic transmission and membrane trafficking. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SYNJ1NM_203446.3 linkuse as main transcriptc.*2291A>G 3_prime_UTR_variant 33/33 ENST00000674351.1 NP_982271.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SYNJ1ENST00000674351.1 linkuse as main transcriptc.*2291A>G 3_prime_UTR_variant 33/33 NM_203446.3 ENSP00000501530 O43426-2

Frequencies

GnomAD3 genomes
AF:
0.127
AC:
19271
AN:
152156
Hom.:
1286
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.119
Gnomad AMI
AF:
0.0822
Gnomad AMR
AF:
0.118
Gnomad ASJ
AF:
0.0928
Gnomad EAS
AF:
0.0471
Gnomad SAS
AF:
0.0778
Gnomad FIN
AF:
0.117
Gnomad MID
AF:
0.0949
Gnomad NFE
AF:
0.147
Gnomad OTH
AF:
0.135
GnomAD4 exome
AF:
0.120
AC:
52
AN:
432
Hom.:
3
Cov.:
0
AF XY:
0.142
AC XY:
37
AN XY:
260
show subpopulations
Gnomad4 FIN exome
AF:
0.122
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.127
AC:
19288
AN:
152274
Hom.:
1287
Cov.:
33
AF XY:
0.123
AC XY:
9186
AN XY:
74472
show subpopulations
Gnomad4 AFR
AF:
0.119
Gnomad4 AMR
AF:
0.118
Gnomad4 ASJ
AF:
0.0928
Gnomad4 EAS
AF:
0.0470
Gnomad4 SAS
AF:
0.0781
Gnomad4 FIN
AF:
0.117
Gnomad4 NFE
AF:
0.147
Gnomad4 OTH
AF:
0.133
Alfa
AF:
0.139
Hom.:
945
Bravo
AF:
0.124
Asia WGS
AF:
0.0520
AC:
181
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.43
CADD
Benign
5.3
DANN
Benign
0.72

Splicing

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: rs7279487; hg19: chr21-34001824; API