chr4-89839677-C-T

Variant names:

• chr4-89839677-C-T
• rs2583988
• ENST00000501215.1:n.1728C>T

Variant summary

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

The ENST00000501215.1(SNCA-AS1):​n.1728C>T 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 0.186 in 152,122 control chromosomes in the GnomAD database, including 3,332 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 (3332 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SNCA-AS1 ENST00000501215.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.337
• Publications: 38 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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: ENST00000501215.1. 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.480+1271C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNCA-AS1	ENST00000501215.1	TSL:2	n.1728C>T		non_coding_transcript_exon	Exon 2 of 2
	SNCA-AS1	ENST00000513653.1	TSL:3	n.473+1271C>T		intron	N/A
	SNCA-AS1	ENST00000777108.1		n.487+1271C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28354 AN: 152004 Hom.: 3330 Cov.: 32

Gnomad AFR AF: 0.0662

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.206

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.186 AC: 28369 AN: 152122 Hom.: 3332 Cov.: 32 AF XY: 0.184 AC XY: 13686 AN XY: 74348

African (AFR) AF: 0.0661 AC: 2747 AN: 41534

American (AMR) AF: 0.177 AC: 2697 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3468

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5172

South Asian (SAS) AF: 0.123 AC: 594 AN: 4820

European-Finnish (FIN) AF: 0.243 AC: 2566 AN: 10560

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18243 AN: 67980

Other (OTH) AF: 0.204 AC: 431 AN: 2108

Alfa AF: 0.192 Hom.: 1240

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	-0.91
CADD	Benign	7.5
DANN	Benign	0.53
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs2583988; hg19: chr4-90760828;