4-89731983-C-T

Position:

• chr4-89731983-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_000345.4(SNCA):​c.307-2706G>A variant causes a intron change. The variant allele was found at a frequency of 0.053 in 152,118 control chromosomes in the GnomAD database, including 309 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 0.053 (309 hom., cov: 32)
• Consequence: SNCA NM_000345.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.30

Genes affected

SNCA (HGNC:11138): (synuclein alpha) Alpha-synuclein is a member of the synuclein family, which also includes beta- and gamma-synuclein. Synucleins are abundantly expressed in the brain and alpha- and beta-synuclein inhibit phospholipase D2 selectively. SNCA may serve to integrate presynaptic signaling and membrane trafficking. Defects in SNCA have been implicated in the pathogenesis of Parkinson disease. SNCA peptides are a major component of amyloid plaques in the brains of patients with Alzheimer's disease. Alternatively spliced transcripts encoding different isoforms have been identified for this gene. [provided by RefSeq, Feb 2016]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.081 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNCA	NM_000345.4	c.307-2706G>A		intron_variant		ENST00000394991.8	NP_000336.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNCA	ENST00000394991.8	c.307-2706G>A		intron_variant		1	NM_000345.4	ENSP00000378442	P1

Frequencies

GnomAD3 genomes AF: 0.0530 AC: 8059 AN: 152000 Hom.: 308 Cov.: 32

Gnomad AFR AF: 0.0152

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0542

Gnomad ASJ AF: 0.0781

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0438

Gnomad FIN AF: 0.0284

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0827

Gnomad OTH AF: 0.0622

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

GnomAD4 genome AF: 0.0530 AC: 8063 AN: 152118 Hom.: 309 Cov.: 32 AF XY: 0.0516 AC XY: 3834 AN XY: 74350

Gnomad4 AFR AF: 0.0152

Gnomad4 AMR AF: 0.0542

Gnomad4 ASJ AF: 0.0781

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0449

Gnomad4 FIN AF: 0.0284

Gnomad4 NFE AF: 0.0828

Gnomad4 OTH AF: 0.0616

Alfa AF: 0.0793 Hom.: 149

Bravo AF: 0.0527

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	5.2
DANN	Benign	0.81

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: rs17180453; hg19: chr4-90653134;