6-83600212-A-T

Position:

• chr6-83600212-A-T

Variant summary

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

The NM_001242792.2(SNAP91):​c.1324+1059T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 152,134 control chromosomes in the GnomAD database, including 45,900 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 0.77 (45900 hom., cov: 32)
• Consequence: SNAP91 NM_001242792.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

SNAP91 (HGNC:14986): (synaptosome associated protein 91) Predicted to enable several functions, including SNARE binding activity; clathrin binding activity; and phosphatidylinositol binding activity. Acts upstream of or within regulation of clathrin-dependent endocytosis. Predicted to be located in several cellular components, including postsynaptic density; presynaptic endosome; and presynaptic membrane. Predicted to be extrinsic component of endosome membrane. Predicted to be active in several cellular components, including Schaffer collateral - CA1 synapse; cytoplasmic vesicle; and parallel fiber to Purkinje cell synapse. Predicted to be extrinsic component of presynaptic endocytic zone membrane. Biomarker of Alzheimer's disease. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNAP91	NM_001242792.2	c.1324+1059T>A		intron_variant		ENST00000369694.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNAP91	ENST00000369694.7	c.1324+1059T>A		intron_variant		5	NM_001242792.2	P4

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117453 AN: 152016 Hom.: 45827 Cov.: 32

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.773 AC: 117589 AN: 152134 Hom.: 45900 Cov.: 32 AF XY: 0.776 AC XY: 57718 AN XY: 74350

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.754

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.739

Alfa AF: 0.751 Hom.: 5379

Bravo AF: 0.775

Asia WGS AF: 0.839 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.017
DANN	Benign	0.37

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: rs9294279; hg19: chr6-84309931;