rs2023238

chr6-83573042-A-Gchr6-83573042-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.2442+1968T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 152,056 control chromosomes in the GnomAD database, including 38,191 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 0.71 (38191 hom., cov: 31)
• Consequence: SNAP91 NM_001242792.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNAP91	NM_001242792.2	c.2442+1968T>C		intron_variant		ENST00000369694.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNAP91	ENST00000369694.7	c.2442+1968T>C		intron_variant		5	NM_001242792.2	P4

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107108 AN: 151938 Hom.: 38149 Cov.: 31

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.705 AC: 107201 AN: 152056 Hom.: 38191 Cov.: 31 AF XY: 0.705 AC XY: 52381 AN XY: 74318

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.665

Alfa AF: 0.670 Hom.: 45051

Bravo AF: 0.694

Asia WGS AF: 0.692 AC: 2407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.77
Dann	Benign	0.44

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: rs2023238; hg19: chr6-84282761;