rs145911562

Positions:

chrX-47607150-T-C

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_006950.3(SYN1):c.426A>G(p.Lys142Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00113 in 1,209,945 control chromosomes in the GnomAD database, including 6 homozygotes. There are 597 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.00067 ( 0 hom., 23 hem., cov: 22)

Exomes 𝑓: 0.0012 ( 6 hom. 574 hem. )

Consequence

SYN1
NM_006950.3 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 2.52

Variant links:

Genes affected

SYN1 (HGNC:11494): (synapsin I) This gene is a member of the synapsin gene family. Synapsins encode neuronal phosphoproteins which associate with the cytoplasmic surface of synaptic vesicles. Family members are characterized by common protein domains, and they are implicated in synaptogenesis and the modulation of neurotransmitter release, suggesting a potential role in several neuropsychiatric diseases. This member of the synapsin family plays a role in regulation of axonogenesis and synaptogenesis. The protein encoded serves as a substrate for several different protein kinases and phosphorylation may function in the regulation of this protein in the nerve terminal. Mutations in this gene may be associated with X-linked disorders with primary neuronal degeneration such as Rett syndrome. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

SYN1 links:

ENSG00000283743 (HGNC:):

ENSG00000283743 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant X-47607150-T-C is Benign according to our data. Variant chrX-47607150-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 207459.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-47607150-T-C is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=2.52 with no splicing effect.

BS2

High Hemizygotes in GnomAd4 at 23 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SYN1	NM_006950.3 linkuse as main transcript	c.426A>G	p.Lys142Lys	synonymous_variant	2/13	ENST00000295987.13	NP_008881.2	P17600-1
SYN1	NM_133499.2 linkuse as main transcript	c.426A>G	p.Lys142Lys	synonymous_variant	2/13		NP_598006.1	P17600-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SYN1	ENST00000295987.13 linkuse as main transcript	c.426A>G	p.Lys142Lys	synonymous_variant	2/13	2	NM_006950.3	ENSP00000295987.7	P17600-1
SYN1	ENST00000340666.5 linkuse as main transcript	c.426A>G	p.Lys142Lys	synonymous_variant	2/13	1		ENSP00000343206.4	P17600-2
SYN1	ENST00000639776.1 linkuse as main transcript	c.84A>G	p.Lys28Lys	synonymous_variant	2/6	3		ENSP00000492521.1	A0A1W2PS00
ENSG00000283743	ENST00000638776.2 linkuse as main transcript	n.2882A>G		non_coding_transcript_exon_variant	8/16	5

Frequencies

GnomAD3 genomes

AF:

0.000678

AC:

AN:

112028

Hom.:

Cov.:

AF XY:

0.000702

AC XY:

AN XY:

34198

show subpopulations

Gnomad AFR

AF:

0.0000325

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000190

Gnomad ASJ

AF:

0.00113

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00554

Gnomad FIN

AF:

0.000985

Gnomad MID

AF:

0.00418

Gnomad NFE

AF:

0.000883

Gnomad OTH

AF:

0.000668

GnomAD3 exomes

AF:

0.00122

AC:

224

AN:

183391

Hom.:

AF XY:

0.00189

AC XY:

128

AN XY:

67853

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000729

Gnomad ASJ exome

AF:

0.000267

Gnomad EAS exome

AF:

0.000144

Gnomad SAS exome

AF:

0.00792

Gnomad FIN exome

AF:

0.000812

Gnomad NFE exome

AF:

0.000586

Gnomad OTH exome

AF:

0.00132

GnomAD4 exome

AF:

0.00117

AC:

1288

AN:

1097866

Hom.:

Cov.:

AF XY:

0.00158

AC XY:

574

AN XY:

363232

show subpopulations

Gnomad4 AFR exome

AF:

0.000152

Gnomad4 AMR exome

AF:

0.000142

Gnomad4 ASJ exome

AF:

0.000361

Gnomad4 EAS exome

AF:

0.0000662

Gnomad4 SAS exome

AF:

0.00939

Gnomad4 FIN exome

AF:

0.000592

Gnomad4 NFE exome

AF:

0.000766

Gnomad4 OTH exome

AF:

0.00158

GnomAD4 genome

AF:

0.000669

AC:

AN:

112079

Hom.:

Cov.:

AF XY:

0.000671

AC XY:

AN XY:

34259

show subpopulations

Gnomad4 AFR

AF:

0.0000324

Gnomad4 AMR

AF:

0.000189

Gnomad4 ASJ

AF:

0.00113

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00556

Gnomad4 FIN

AF:

0.000985

Gnomad4 NFE

AF:

0.000883

Gnomad4 OTH

AF:

0.000659

Alfa

AF:

0.000618

Hom.:

Bravo

AF:

0.000434

EpiCase

AF:

0.000872

EpiControl

AF:

0.000771

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	GeneDx	May 20, 2015	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Likely benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Jun 05, 2018	- -

not provided

Benign:2

Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Likely benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -

Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 27, 2024

- -

History of neurodevelopmental disorder

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

May 31, 2016

Synonymous alterations with insufficient evidence to classify as benign -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

DANN

Benign

0.68

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.12

Details are displayed if max score is > 0.2

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over