rs62192181

chr2-232418305-A-T

Variant summary

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

The ENST00000373592.2(ECEL1P1):n.852-14T>A variant causes a splice polypyrimidine tract, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 561,020 control chromosomes in the GnomAD database, including 17,704 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 0.21 (4190 hom., cov: 32)
  • Exomes 𝑓: 0.25 (13514 hom.)
• Consequence: ECEL1P1 ENST00000373592.2 splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41

Genes affected

ECEL1P1 (HGNC:14017): (endothelin converting enzyme like 1 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ECEL1P1	ENST00000373592.2	n.852-14T>A		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31958 AN: 151976 Hom.: 4188 Cov.: 32

Gnomad AFR AF: 0.0664

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.0968

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.231

GnomAD4 exome AF: 0.247 AC: 101139 AN: 408926 Hom.: 13514 Cov.: 0 AF XY: 0.246 AC XY: 56019 AN XY: 227374

Gnomad4 AFR exome AF: 0.0666

Gnomad4 AMR exome AF: 0.177

Gnomad4 ASJ exome AF: 0.324

Gnomad4 EAS exome AF: 0.101

Gnomad4 SAS exome AF: 0.200

Gnomad4 FIN exome AF: 0.255

Gnomad4 NFE exome AF: 0.285

Gnomad4 OTH exome AF: 0.248

GnomAD4 genome AF: 0.210 AC: 31949 AN: 152094 Hom.: 4190 Cov.: 32 AF XY: 0.209 AC XY: 15505 AN XY: 74334

Gnomad4 AFR AF: 0.0662

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.0964

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.229

Alfa AF: 0.237 Hom.: 570

Bravo AF: 0.201

Asia WGS AF: 0.140 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.95
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs62192181; hg19: chr2-233283015; COSMIC: COSV65301653;