ENST00000442636.2:n.418G>A

Variant names:

• chr1-8879783-G-A
• rs1325920
• ENST00000442636.2:n.418G>A

Variant summary

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

The ENST00000442636.2(ENO1-AS1):​n.418G>A 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 0.779 in 152,124 control chromosomes in the GnomAD database, including 46,790 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 0.78 (46789 hom., cov: 33)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: ENO1-AS1 ENST00000442636.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103
• Publications: 6 publications found

Genes affected

ENO1-AS1 (HGNC:40214): (ENO1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENO1-AS1	NR_038351.1	n.345G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENO1-AS1	ENST00000442636.2	n.418G>A		non_coding_transcript_exon_variant	Exon 2 of 2	2
ENO1-AS1	ENST00000835134.1	n.427G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENO1-AS1	ENST00000835135.1	n.308G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENO1-AS1	ENST00000835136.1	n.311G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.779 AC: 118423 AN: 152000 Hom.: 46764 Cov.: 33

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.787

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

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) AF: 1.00 AC: 2 AN: 2

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.779 AC: 118499 AN: 152120 Hom.: 46789 Cov.: 33 AF XY: 0.781 AC XY: 58087 AN XY: 74378

African (AFR) AF: 0.640 AC: 26507 AN: 41432

American (AMR) AF: 0.841 AC: 12846 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2378 AN: 3468

East Asian (EAS) AF: 0.937 AC: 4855 AN: 5182

South Asian (SAS) AF: 0.727 AC: 3509 AN: 4828

European-Finnish (FIN) AF: 0.851 AC: 9018 AN: 10596

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.833 AC: 56677 AN: 68016

Other (OTH) AF: 0.789 AC: 1668 AN: 2114

Alfa AF: 0.812 Hom.: 25506

Bravo AF: 0.775

Asia WGS AF: 0.797 AC: 2774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.8
DANN	Benign	0.77
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs1325920; hg19: chr1-8939842;