chr6-83622122-C-G

Variant names:

• chr6-83622122-C-G
• rs3798867
• NM_001242792.2:c.807+1179G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001242792.2(SNAP91):​c.807+1179G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,700 control chromosomes in the GnomAD database, including 11,542 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 0.38 (11542 hom., cov: 32)
• Consequence: SNAP91 NM_001242792.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001242792.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNAP91	NM_001242792.2	MANE Select	c.807+1179G>C		intron	N/A	NP_001229721.1
	SNAP91	NM_014841.3		c.807+1179G>C		intron	N/A	NP_055656.1
	SNAP91	NM_001376675.1		c.807+1179G>C		intron	N/A	NP_001363604.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNAP91	ENST00000369694.7	TSL:5 MANE Select	c.807+1179G>C		intron	N/A	ENSP00000358708.2
	SNAP91	ENST00000520302.5	TSL:1	c.807+1179G>C		intron	N/A	ENSP00000428511.1
	SNAP91	ENST00000520213.5	TSL:1	c.766-5083G>C		intron	N/A	ENSP00000428026.1

Frequencies

GnomAD3 genomes AF: 0.382 AC: 57917 AN: 151584 Hom.: 11538 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.382 AC: 57937 AN: 151700 Hom.: 11542 Cov.: 32 AF XY: 0.385 AC XY: 28515 AN XY: 74130

African (AFR) AF: 0.265 AC: 10975 AN: 41394

American (AMR) AF: 0.369 AC: 5623 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1225 AN: 3464

East Asian (EAS) AF: 0.417 AC: 2159 AN: 5176

South Asian (SAS) AF: 0.500 AC: 2406 AN: 4810

European-Finnish (FIN) AF: 0.481 AC: 5046 AN: 10494

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29414 AN: 67800

Other (OTH) AF: 0.360 AC: 755 AN: 2098

Alfa AF: 0.407 Hom.: 1583

Bravo AF: 0.365

Asia WGS AF: 0.473 AC: 1626 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.049
DANN	Benign	0.34
PhyloP100		-2.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3798867; hg19: chr6-84331841;