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6-83560894-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_001242792.2(SNAP91):c.2496G>A(p.Ser832=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00424 in 1,613,762 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0033 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0043 ( 23 hom. )

Consequence

SNAP91
NM_001242792.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.22
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 6-83560894-C-T is Benign according to our data. Variant chr6-83560894-C-T is described in ClinVar as [Benign]. Clinvar id is 713594.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=1.22 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 2 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SNAP91NM_001242792.2 linkuse as main transcriptc.2496G>A p.Ser832= synonymous_variant 27/30 ENST00000369694.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SNAP91ENST00000369694.7 linkuse as main transcriptc.2496G>A p.Ser832= synonymous_variant 27/305 NM_001242792.2 P4O60641-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00328
AC:
499
AN:
152160
Hom.:
2
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000772
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00249
Gnomad ASJ
AF:
0.00259
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000622
Gnomad FIN
AF:
0.00264
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.00561
Gnomad OTH
AF:
0.00192
GnomAD3 exomes
AF:
0.00299
AC:
743
AN:
248772
Hom.:
2
AF XY:
0.00302
AC XY:
408
AN XY:
134958
show subpopulations
Gnomad AFR exome
AF:
0.000581
Gnomad AMR exome
AF:
0.00142
Gnomad ASJ exome
AF:
0.00199
Gnomad EAS exome
AF:
0.0000557
Gnomad SAS exome
AF:
0.00118
Gnomad FIN exome
AF:
0.00260
Gnomad NFE exome
AF:
0.00491
Gnomad OTH exome
AF:
0.00298
GnomAD4 exome
AF:
0.00434
AC:
6347
AN:
1461484
Hom.:
23
Cov.:
30
AF XY:
0.00431
AC XY:
3135
AN XY:
727032
show subpopulations
Gnomad4 AFR exome
AF:
0.000986
Gnomad4 AMR exome
AF:
0.00143
Gnomad4 ASJ exome
AF:
0.00176
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00109
Gnomad4 FIN exome
AF:
0.00292
Gnomad4 NFE exome
AF:
0.00512
Gnomad4 OTH exome
AF:
0.00421
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00328
AC:
499
AN:
152278
Hom.:
2
Cov.:
33
AF XY:
0.00330
AC XY:
246
AN XY:
74450
show subpopulations
Gnomad4 AFR
AF:
0.000770
Gnomad4 AMR
AF:
0.00248
Gnomad4 ASJ
AF:
0.00259
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000622
Gnomad4 FIN
AF:
0.00264
Gnomad4 NFE
AF:
0.00562
Gnomad4 OTH
AF:
0.00190
Alfa
AF:
0.00494
Hom.:
4
Bravo
AF:
0.00302
Asia WGS
AF:
0.000866
AC:
3
AN:
3478
EpiCase
AF:
0.00420
EpiControl
AF:
0.00474

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJul 29, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.41
Cadd
Benign
5.6
Dann
Benign
0.38

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs187423527; hg19: chr6-84270613; API