rs10002435

Positions:

• chr4-89791360-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000345.4(SNCA):​c.306+30886C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 94,198 control chromosomes in the GnomAD database, including 2,932 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 0.27 (2932 hom., cov: 27)
• Consequence: SNCA NM_000345.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNCA	NM_000345.4	c.306+30886C>T		intron_variant		ENST00000394991.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNCA	ENST00000394991.8	c.306+30886C>T		intron_variant		1	NM_000345.4	P1

Frequencies

GnomAD3 genomes AF: 0.274 AC: 25748 AN: 94120 Hom.: 2927 Cov.: 27

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.274 AC: 25772 AN: 94198 Hom.: 2932 Cov.: 27 AF XY: 0.271 AC XY: 12520 AN XY: 46220

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.264

Alfa AF: 0.121 Hom.: 261

Bravo AF: 0.184

Asia WGS AF: 0.208 AC: 712 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.5
DANN	Benign	0.58

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: rs10002435; hg19: chr4-90712511;