rs1325920

Positions:

• chr1-8879783-G-A
• chr1-8879783-G-C
• chr1-8879783-G-T

Variant summary

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

The NR_038351.1(ENO1-AS1):​n.345G>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 NR_038351.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ENO1-AS1	NR_038351.1	n.345G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENO1-AS1	ENST00000442636.1	n.345G>A		non_coding_transcript_exon_variant	2/2	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

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.500

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

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.841

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.851

Gnomad4 NFE AF: 0.833

Gnomad4 OTH AF: 0.789

Alfa AF: 0.811 Hom.: 22920

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1325920; hg19: chr1-8939842;