dbSNP rs1010: VAMP8:c.*143T>C (chr2-85581859-T-C) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003761.5(VAMP8):c.*143T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 1,133,830 control chromosomes in the GnomAD database, including 95,968 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.45 ( 15903 hom., cov: 30)

Exomes 𝑓: 0.40 ( 80065 hom. )

Consequence

VAMP8
NM_003761.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0580

Variant links:

Genes affected

VAMP8 (HGNC:12647): (vesicle associated membrane protein 8) This gene encodes an integral membrane protein that belongs to the synaptobrevin/vesicle-associated membrane protein subfamily of soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs). The encoded protein is involved in the fusion of synaptic vesicles with the presynaptic membrane.[provided by RefSeq, Jun 2010]

VAMP8 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 2-85581859-T-C is Benign according to our data. Variant chr2-85581859-T-C is described in ClinVar as [Benign]. Clinvar id is 1182311.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VAMP8	NM_003761.5 link	c.*143T>C		3_prime_UTR_variant	Exon 3 of 3	ENST00000263864.10	NP_003752.2	Q9BV40
VAMP8	XM_017005170.2 link	c.*279T>C		3_prime_UTR_variant	Exon 4 of 4		XP_016860659.1	B8ZZT4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
VAMP8	ENST00000263864.10 link	c.*143T>C	3_prime_UTR_variant	Exon 3 of 3	1	NM_003761.5	ENSP00000263864.5	Q9BV40
VAMP8	ENST00000409760.1 link	c.*279T>C	3_prime_UTR_variant	Exon 4 of 4	3		ENSP00000387094.1	B8ZZT4
VAMP8	ENST00000432071.1 link	c.*143T>C	3_prime_UTR_variant	Exon 3 of 3	3		ENSP00000407984.1	C9JXZ5

Frequencies

GnomAD3 genomes

AF:

0.451

AC:

68489

AN:

151694

Hom.:

15880

Cov.:

show subpopulations

Gnomad AFR

AF:

0.563

Gnomad AMI

AF:

0.457

Gnomad AMR

AF:

0.375

Gnomad ASJ

AF:

0.361

Gnomad EAS

AF:

0.386

Gnomad SAS

AF:

0.378

Gnomad FIN

AF:

0.441

Gnomad MID

AF:

0.357

Gnomad NFE

AF:

0.418

Gnomad OTH

AF:

0.432

GnomAD4 exome

AF:

0.402

AC:

395243

AN:

982016

Hom.:

80065

Cov.:

AF XY:

0.403

AC XY:

200056

AN XY:

496772

show subpopulations

Gnomad4 AFR exome

AF:

0.549

Gnomad4 AMR exome

AF:

0.309

Gnomad4 ASJ exome

AF:

0.366

Gnomad4 EAS exome

AF:

0.371

Gnomad4 SAS exome

AF:

0.370

Gnomad4 FIN exome

AF:

0.423

Gnomad4 NFE exome

AF:

0.405

Gnomad4 OTH exome

AF:

0.416

GnomAD4 genome

AF:

0.452

AC:

68561

AN:

151814

Hom.:

15903

Cov.:

AF XY:

0.450

AC XY:

33391

AN XY:

74186

show subpopulations

Gnomad4 AFR

AF:

0.563

Gnomad4 AMR

AF:

0.374

Gnomad4 ASJ

AF:

0.361

Gnomad4 EAS

AF:

0.386

Gnomad4 SAS

AF:

0.379

Gnomad4 FIN

AF:

0.441

Gnomad4 NFE

AF:

0.418

Gnomad4 OTH

AF:

0.435

Alfa

AF:

0.413

Hom.:

14248

Bravo

AF:

0.452

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Nov 02, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 25691096) -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.5

DANN

Benign

0.36

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over