rs62192181

Variant names:

• chr2-232418305-A-T
• rs62192181
• ENST00000836067.1:n.789T>A

Variant summary

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

The ENST00000836067.1(ENSG00000237087):​n.789T>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 0.237 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: ENSG00000237087 ENST00000836067.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41
• Publications: 2 publications found

Genes affected

ENSG00000237087 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ECEL1P1		n.232418305A>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000237087	ENST00000836067.1	n.789T>A		non_coding_transcript_exon_variant	Exon 4 of 5
ENSG00000237087	ENST00000836080.1	n.383T>A		non_coding_transcript_exon_variant	Exon 2 of 3
ECEL1P1	ENST00000373592.2	n.852-14T>A		intron_variant	Intron 2 of 8	6

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

African (AFR) AF: 0.0666 AC: 787 AN: 11808

American (AMR) AF: 0.177 AC: 5723 AN: 32384

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 4569 AN: 14112

East Asian (EAS) AF: 0.101 AC: 1704 AN: 16880

South Asian (SAS) AF: 0.200 AC: 12478 AN: 62386

European-Finnish (FIN) AF: 0.255 AC: 5381 AN: 21070

Middle Eastern (MID) AF: 0.256 AC: 824 AN: 3220

European-Non Finnish (NFE) AF: 0.285 AC: 64510 AN: 226232

Other (OTH) AF: 0.248 AC: 5163 AN: 20834

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

African (AFR) AF: 0.0662 AC: 2749 AN: 41522

American (AMR) AF: 0.201 AC: 3072 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1217 AN: 3472

East Asian (EAS) AF: 0.0964 AC: 497 AN: 5154

South Asian (SAS) AF: 0.194 AC: 934 AN: 4816

European-Finnish (FIN) AF: 0.261 AC: 2761 AN: 10572

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19753 AN: 67942

Other (OTH) AF: 0.229 AC: 484 AN: 2110

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
PhyloP100		-2.4

Splicing

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

Other links and lift over

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