rs55781386

chr2-232386358-G-C

Variant summary

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

The NR_028501.1(ECEL1P2):n.687C>G 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 0.206 in 224,926 control chromosomes in the GnomAD database, including 5,716 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 0.20 (3741 hom., cov: 32)
  • Exomes 𝑓: 0.22 (1975 hom.)
• Consequence: ECEL1P2 NR_028501.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.824

Genes affected

ECEL1P2 (HGNC:14019): (endothelin converting enzyme like 1 pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ECEL1P2	NR_028501.1	n.687C>G		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ECEL1P2	ENST00000461596.1	n.687C>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30480 AN: 151994 Hom.: 3738 Cov.: 32

Gnomad AFR AF: 0.0763

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.0959

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.229

GnomAD4 exome AF: 0.217 AC: 15771 AN: 72814 Hom.: 1975 Cov.: 0 AF XY: 0.211 AC XY: 8009 AN XY: 37878

Gnomad4 AFR exome AF: 0.0458

Gnomad4 AMR exome AF: 0.180

Gnomad4 ASJ exome AF: 0.258

Gnomad4 EAS exome AF: 0.0859

Gnomad4 SAS exome AF: 0.169

Gnomad4 FIN exome AF: 0.185

Gnomad4 NFE exome AF: 0.241

Gnomad4 OTH exome AF: 0.212

GnomAD4 genome AF: 0.200 AC: 30486 AN: 152112 Hom.: 3741 Cov.: 32 AF XY: 0.198 AC XY: 14739 AN XY: 74348

Gnomad4 AFR AF: 0.0765

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.0957

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.228

Alfa AF: 0.228 Hom.: 531

Bravo AF: 0.194

Asia WGS AF: 0.136 AC: 475 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	9.7
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55781386; hg19: chr2-233251068;