Genetic Variant ENST00000822161.1:n.56+37C>T (chr6-158099285-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000822161.1(ENSG00000306953):n.56+37C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 151,850 control chromosomes in the GnomAD database, including 38,213 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 0.70 ( 38201 hom., cov: 30)

Exomes 𝑓: 0.61 ( 12 hom. )

Consequence

ENSG00000306953
ENST00000822161.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.306

Publications

2 publications found

Variant links:

Genes affected

ENSG00000306953 (HGNC:):

ENSG00000306953 links:

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]

SYNJ2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000822161.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SYNJ2	NM_003898.4	MANE Select	c.*2921C>T	downstream_gene	N/A	NP_003889.1
SYNJ2	NM_001410947.1		c.*3695C>T	downstream_gene	N/A	NP_001397876.1
SYNJ2	NM_001178088.2		c.*2921C>T	downstream_gene	N/A	NP_001171559.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ENSG00000306953	ENST00000822161.1		n.56+37C>T	intron	N/A
SYNJ2	ENST00000355585.9	TSL:1 MANE Select	c.*2921C>T	downstream_gene	N/A	ENSP00000347792.4
SYNJ2	ENST00000638626.1	TSL:1	c.*2921C>T	downstream_gene	N/A	ENSP00000492369.1

Frequencies

GnomAD3 genomes

AF:

0.696

AC:

105592

AN:

151666

Hom.:

38161

Cov.:

show subpopulations

Gnomad AFR

AF:

0.896

Gnomad AMI

AF:

0.757

Gnomad AMR

AF:

0.484

Gnomad ASJ

AF:

0.615

Gnomad EAS

AF:

0.585

Gnomad SAS

AF:

0.686

Gnomad FIN

AF:

0.632

Gnomad MID

AF:

0.631

Gnomad NFE

AF:

0.646

Gnomad OTH

AF:

0.663

GnomAD4 exome

AF:

0.606

AC:

AN:

Hom.:

AF XY:

0.583

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.586

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.696

AC:

105671

AN:

151784

Hom.:

38201

Cov.:

AF XY:

0.691

AC XY:

51235

AN XY:

74178

show subpopulations

African (AFR)

AF:

0.896

AC:

37150

AN:

41442

American (AMR)

AF:

0.483

AC:

7367

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.615

AC:

2130

AN:

3464

East Asian (EAS)

AF:

0.585

AC:

3028

AN:

5172

South Asian (SAS)

AF:

0.684

AC:

3287

AN:

4806

European-Finnish (FIN)

AF:

0.632

AC:

6609

AN:

10454

Middle Eastern (MID)

AF:

0.622

AC:

183

AN:

294

European-Non Finnish (NFE)

AF:

0.646

AC:

43832

AN:

67886

Other (OTH)

AF:

0.661

AC:

1395

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1468

2937

4405

5874

7342

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

822

1644

2466

3288

4110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.674

Hom.:

4430

Bravo

AF:

0.691

Asia WGS

AF:

0.656

AC:

2282

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.69

(source)

DANN

Benign

0.77

PhyloP100

-0.31

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over