rs2619366

Variant names:

• chr4-89842109-A-G
• rs2619366
• ENST00000777108.1:n.886A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000777108.1(SNCA-AS1):​n.886A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,200 control chromosomes in the GnomAD database, including 3,448 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 0.19 (3448 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SNCA-AS1 ENST00000777108.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 3 publications found

Genes affected

SNCA-AS1 (HGNC:50600): (SNCA antisense RNA 1)

ENSG00000301182 (HGNC:58852):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000777108.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNCA-AS1	NR_045481.1		n.*118A>G		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNCA-AS1	ENST00000777108.1		n.886A>G		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000301182	ENST00000776860.1		n.209-1147T>C		intron	N/A
	ENSG00000301182	ENST00000776861.1		n.183-1147T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29522 AN: 152082 Hom.: 3445 Cov.: 32

Gnomad AFR AF: 0.0930

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.194 AC: 29543 AN: 152200 Hom.: 3448 Cov.: 32 AF XY: 0.192 AC XY: 14268 AN XY: 74420

African (AFR) AF: 0.0930 AC: 3862 AN: 41522

American (AMR) AF: 0.179 AC: 2732 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 714 AN: 3472

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5184

South Asian (SAS) AF: 0.124 AC: 596 AN: 4824

European-Finnish (FIN) AF: 0.243 AC: 2571 AN: 10598

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18242 AN: 67988

Other (OTH) AF: 0.211 AC: 445 AN: 2112

Alfa AF: 0.224 Hom.: 533

Bravo AF: 0.188

Asia WGS AF: 0.0620 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.0
DANN	Benign	0.84
PhyloP100		-0.092

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2619366;

hg19: chr4-90763260;