rs217325

Variant names:

• chr6-83640935-C-G
• rs217325
• NM_001242792.2:c.765+161G>C

Your query was ambiguous. Multiple possible variants found:

• chr6-83640935-C-G
• chr6-83640935-C-T

Variant summary

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

The NM_001242792.2(SNAP91):​c.765+161G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 151,904 control chromosomes in the GnomAD database, including 43,559 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 0.75 (43559 hom., cov: 31)
• Consequence: SNAP91 NM_001242792.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNAP91	NM_001242792.2	c.765+161G>C		intron_variant	Intron 8 of 29	ENST00000369694.7	NP_001229721.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNAP91	ENST00000369694.7	c.765+161G>C		intron_variant	Intron 8 of 29	5	NM_001242792.2	ENSP00000358708.2

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114389 AN: 151786 Hom.: 43523 Cov.: 31

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.754 AC: 114476 AN: 151904 Hom.: 43559 Cov.: 31 AF XY: 0.759 AC XY: 56371 AN XY: 74264

Gnomad4 AFR AF: 0.660

Gnomad4 AMR AF: 0.804

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.955

Gnomad4 SAS AF: 0.878

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.735

Alfa AF: 0.766 Hom.: 5581

Bravo AF: 0.746

Asia WGS AF: 0.889 AC: 3092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.58
DANN	Benign	0.41

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: rs217325; hg19: chr6-84350654;