X-47573982-TGCTGTAGGGGTC-A

Variant names:

• chrX-47573982-TGCTGTAGGGGTC-A
• NM_006950.3:c.1982+8_1982+20delGACCCCTACAGCAinsT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP6_Moderate

The NM_006950.3(SYN1):​c.1982+8_1982+20delGACCCCTACAGCAinsT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 23)
• Consequence: SYN1 NM_006950.3 splice_region, intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.57

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant X-47573982-TGCTGTAGGGGTC-A is Benign according to our data. Variant chrX-47573982-TGCTGTAGGGGTC-A is described in ClinVar as [Likely_benign]. Clinvar id is 3010198.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SYN1	NM_006950.3	c.1982+8_1982+20delGACCCCTACAGCAinsT		splice_region_variant, intron_variant	Intron 12 of 12	ENST00000295987.13	NP_008881.2
SYN1	NM_133499.2	c.1982+8_1982+20delGACCCCTACAGCAinsT		splice_region_variant, intron_variant	Intron 12 of 12		NP_598006.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SYN1	ENST00000295987.13	c.1982+8_1982+20delGACCCCTACAGCAinsT		splice_region_variant, intron_variant	Intron 12 of 12	2	NM_006950.3	ENSP00000295987.7
SYN1	ENST00000340666.5	c.1982+8_1982+20delGACCCCTACAGCAinsT		splice_region_variant, intron_variant	Intron 12 of 12	1		ENSP00000343206.4
SYN1	ENST00000640721.1	c.70+694_70+706delGACCCCTACAGCAinsT		intron_variant	Intron 1 of 1	5		ENSP00000492857.1

Frequencies

GnomAD3 genomes Cov.: 23

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

GnomAD4 genome Cov.: 23

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

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

Aug 09, 2022

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-47433381;