NM_001975.3:c.865+191C>T

Variant names:

• chr12-6919954-C-T
• rs3213434
• NM_001975.3:c.865+191C>T

Variant summary

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

The NM_001975.3(ENO2):​c.865+191C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,874 control chromosomes in the GnomAD database, including 7,281 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 0.31 (7281 hom., cov: 30)
• Consequence: ENO2 NM_001975.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830
• Publications: 8 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENO2	NM_001975.3	c.865+191C>T		intron_variant	Intron 8 of 11	ENST00000229277.6	NP_001966.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENO2	ENST00000229277.6	c.865+191C>T		intron_variant	Intron 8 of 11	1	NM_001975.3	ENSP00000229277.1

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46967 AN: 151756 Hom.: 7278 Cov.: 30

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.330

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.309 AC: 46977 AN: 151874 Hom.: 7281 Cov.: 30 AF XY: 0.306 AC XY: 22744 AN XY: 74248

African (AFR) AF: 0.351 AC: 14537 AN: 41374

American (AMR) AF: 0.278 AC: 4245 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 928 AN: 3472

East Asian (EAS) AF: 0.234 AC: 1210 AN: 5166

South Asian (SAS) AF: 0.324 AC: 1562 AN: 4814

European-Finnish (FIN) AF: 0.252 AC: 2655 AN: 10548

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.303 AC: 20615 AN: 67934

Other (OTH) AF: 0.333 AC: 703 AN: 2110

Alfa AF: 0.306 Hom.: 888

Bravo AF: 0.309

Asia WGS AF: 0.309 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.40
PhyloP100		-0.083
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3213434; hg19: chr12-7029118;