rs10849541

Positions:

• chr12-6923378-G-A

Variant summary

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

The NM_001975.3(ENO2):​c.*578G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0514 in 152,070 control chromosomes in the GnomAD database, including 582 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 0.051 (582 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENO2 NM_001975.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.73

Genes affected

ENO2 (HGNC:3353): (enolase 2) This gene encodes one of the three enolase isoenzymes found in mammals. This isoenzyme, a homodimer, is found in mature neurons and cells of neuronal origin. A switch from alpha enolase to gamma enolase occurs in neural tissue during development in rats and primates. [provided by RefSeq, Jul 2008]

LOC124902868 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENO2	NM_001975.3	c.*578G>A		3_prime_UTR_variant	12/12	ENST00000229277.6	NP_001966.1
LOC124902868	XR_007063194.1	n.2918C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENO2	ENST00000229277.6	c.*578G>A		3_prime_UTR_variant	12/12	1	NM_001975.3	ENSP00000229277.1
ENO2	ENST00000535366.5	c.*578G>A		3_prime_UTR_variant	11/11	1		ENSP00000437402.1
ENO2	ENST00000541477.5	c.*578G>A		3_prime_UTR_variant	12/12	2		ENSP00000438873.1
ENO2	ENST00000545045.6	c.*578G>A		3_prime_UTR_variant	10/10	5		ENSP00000438062.1

Frequencies

GnomAD3 genomes AF: 0.0514 AC: 7805 AN: 151952 Hom.: 577 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0273

Gnomad ASJ AF: 0.00664

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.0130

Gnomad FIN AF: 0.0000943

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00212

Gnomad OTH AF: 0.0498

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 108 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 58

Gnomad4 AMR exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0514 AC: 7822 AN: 152070 Hom.: 582 Cov.: 32 AF XY: 0.0512 AC XY: 3808 AN XY: 74348

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.0272

Gnomad4 ASJ AF: 0.00664

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.0129

Gnomad4 FIN AF: 0.0000943

Gnomad4 NFE AF: 0.00212

Gnomad4 OTH AF: 0.0502

Alfa AF: 0.0133 Hom.: 167

Bravo AF: 0.0593

Asia WGS AF: 0.0810 AC: 283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.67
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10849541; hg19: chr12-7032541;