rs2736995

chr4-89841046-A-C

Variant summary

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

The NR_045481.1(SNCA-AS1):n.481-295A>C variant causes a intron, non coding transcript 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 NR_045481.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNCA-AS1	NR_045481.1	n.481-295A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNCA-AS1	ENST00000513653.1	n.474-295A>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0662

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.000968

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.204

Alfa AF: 0.234 Hom.: 1129

Bravo AF: 0.179

Asia WGS AF: 0.0610 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.3
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2736995; hg19: chr4-90762197;