12-79087591-G-A

Position:

• chr12-79087591-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005639.3(SYT1):​c.-18+40229G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 151,928 control chromosomes in the GnomAD database, including 1,858 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 0.15 (1858 hom., cov: 32)
• Consequence: SYT1 NM_005639.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930

Genes affected

SYT1 (HGNC:11509): (synaptotagmin 1) This gene encodes a member of the synaptotagmin protein family. The synaptotagmins are integral membrane proteins of synaptic vesicles that serve as calcium sensors in the process of vesicular trafficking and exocytosis. The encoded protein participates in triggering neurotransmitter release at the synapse in response to calcium binding. Mutations in this gene are associated with Baker-Gordon syndrome. [provided by RefSeq, Jan 2023]

LOC105369863 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYT1	NM_005639.3	c.-18+40229G>A		intron_variant		ENST00000261205.9
LOC105369863	XR_007063385.1	n.11858C>T		non_coding_transcript_exon_variant	3/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYT1	ENST00000261205.9	c.-18+40229G>A		intron_variant		1	NM_005639.3	P3

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22951 AN: 151812 Hom.: 1839 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.151 AC: 23009 AN: 151928 Hom.: 1858 Cov.: 32 AF XY: 0.154 AC XY: 11434 AN XY: 74234

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.164

Alfa AF: 0.137 Hom.: 1753

Bravo AF: 0.148

Asia WGS AF: 0.177 AC: 616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.91
DANN	Benign	0.21

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: rs12300068; hg19: chr12-79481371;