22-20861118-GTTTTTT-GTTTTTTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_004782.4(SNAP29):c.237+1789dup variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (3057 hom., cov: 0)
• Consequence: SNAP29 NM_004782.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.487

Genes affected

SNAP29 (HGNC:11133): (synaptosome associated protein 29) This gene, a member of the SNAP25 gene family, encodes a protein involved in multiple membrane trafficking steps. Two other members of this gene family, SNAP23 and SNAP25, encode proteins that bind a syntaxin protein and mediate synaptic vesicle membrane docking and fusion to the plasma membrane. The protein encoded by this gene binds tightly to multiple syntaxins and is localized to intracellular membrane structures rather than to the plasma membrane. While the protein is mostly membrane-bound, a significant fraction of it is found free in the cytoplasm. Use of multiple polyadenylation sites has been noted for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNAP29	NM_004782.4	c.237+1789dup		intron_variant		ENST00000215730.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNAP29	ENST00000215730.12	c.237+1789dup		intron_variant		1	NM_004782.4	P1
SNAP29	ENST00000439214.1	c.-43+1496dup		intron_variant		3
SNAP29	ENST00000490458.1	n.267+1789dup		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.121 AC: 14767 AN: 121750 Hom.: 3057 Cov.: 0

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.00119

Gnomad AMR AF: 0.0560

Gnomad ASJ AF: 0.0183

Gnomad EAS AF: 0.0576

Gnomad SAS AF: 0.0226

Gnomad FIN AF: 0.0135

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0130

Gnomad OTH AF: 0.0968

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

GnomAD4 genome AF: 0.121 AC: 14772 AN: 121750 Hom.: 3057 Cov.: 0 AF XY: 0.121 AC XY: 6928 AN XY: 57454

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.0559

Gnomad4 ASJ AF: 0.0183

Gnomad4 EAS AF: 0.0573

Gnomad4 SAS AF: 0.0224

Gnomad4 FIN AF: 0.0135

Gnomad4 NFE AF: 0.0130

Gnomad4 OTH AF: 0.0990

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs362237; hg19: chr22-21215406;