rs3748971

chr2-232385973-C-T

Variant summary

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

The NR_028501.1(ECEL1P2):n.1072G>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 0.0598 in 152,286 control chromosomes in the GnomAD database, including 367 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 0.060 (366 hom., cov: 32)
  • Exomes 𝑓: 0.067 (1 hom.)
• Consequence: ECEL1P2 NR_028501.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

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 (EAS) allele frequency at 95% confidence interval = 0.084 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ECEL1P2	NR_028501.1	n.1072G>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ECEL1P2	ENST00000461596.1	n.1072G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0598 AC: 9101 AN: 152078 Hom.: 366 Cov.: 32

Gnomad AFR AF: 0.0130

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0489

Gnomad ASJ AF: 0.0919

Gnomad EAS AF: 0.0912

Gnomad SAS AF: 0.0740

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0786

Gnomad OTH AF: 0.0540

GnomAD4 exome AF: 0.0667 AC: 6 AN: 90 Hom.: 1 Cov.: 0 AF XY: 0.0682 AC XY: 3 AN XY: 44

Gnomad4 AMR exome AF: 0.00

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.0606

Gnomad4 OTH exome AF: 0.100

GnomAD4 genome AF: 0.0598 AC: 9095 AN: 152196 Hom.: 366 Cov.: 32 AF XY: 0.0610 AC XY: 4537 AN XY: 74400

Gnomad4 AFR AF: 0.0130

Gnomad4 AMR AF: 0.0489

Gnomad4 ASJ AF: 0.0919

Gnomad4 EAS AF: 0.0908

Gnomad4 SAS AF: 0.0742

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.0785

Gnomad4 OTH AF: 0.0534

Alfa AF: 0.0734 Hom.: 643

Bravo AF: 0.0535

Asia WGS AF: 0.0730 AC: 253 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	3.4
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3748971; hg19: chr2-233250683;