4-89841046-A-C

Variant names:

• chr4-89841046-A-C
• rs2736995
• ENST00000513653.1:n.474-295A>C

Variant summary

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

The ENST00000513653.1(SNCA-AS1):​n.474-295A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 151,930 control chromosomes in the GnomAD database, including 3,325 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 (3325 hom., cov: 31)
• Consequence: SNCA-AS1 ENST00000513653.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960
• Publications: 12 publications found

Genes affected

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

ENSG00000301182 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• 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: ENST00000513653.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNCA-AS1	NR_045481.1		n.481-295A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNCA-AS1	ENST00000513653.1	TSL:3	n.474-295A>C		intron	N/A
	ENSG00000301182	ENST00000776860.1		n.209-84T>G		intron	N/A
	ENSG00000301182	ENST00000776861.1		n.183-84T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28318 AN: 151812 Hom.: 3323 Cov.: 31

Gnomad AFR AF: 0.0663

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.000966

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.147

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.186 AC: 28333 AN: 151930 Hom.: 3325 Cov.: 31 AF XY: 0.184 AC XY: 13664 AN XY: 74236

African (AFR) AF: 0.0662 AC: 2745 AN: 41482

American (AMR) AF: 0.176 AC: 2682 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 714 AN: 3470

East Asian (EAS) AF: 0.000968 AC: 5 AN: 5164

South Asian (SAS) AF: 0.123 AC: 589 AN: 4790

European-Finnish (FIN) AF: 0.243 AC: 2563 AN: 10542

Middle Eastern (MID) AF: 0.155 AC: 45 AN: 290

European-Non Finnish (NFE) AF: 0.268 AC: 18232 AN: 67940

Other (OTH) AF: 0.204 AC: 430 AN: 2104

Alfa AF: 0.222 Hom.: 1823

Bravo AF: 0.179

Asia WGS AF: 0.0610 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.45
PhyloP100		0.096

Splicing

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

Other links and lift over

dbSNP: rs2736995; hg19: chr4-90762197;