rs62192178

Variant names:

• chr2-232415759-G-A
• rs62192178
• ENST00000836062.1:n.289-2156C>T

Variant summary

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

The ENST00000836062.1(ENSG00000237087):​n.289-2156C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 171,222 control chromosomes in the GnomAD database, including 4,857 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 (4240 hom., cov: 33)
  • Exomes 𝑓: 0.23 (617 hom.)
• Consequence: ENSG00000237087 ENST00000836062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000237087	ENST00000836062.1	n.289-2156C>T		intron_variant	Intron 3 of 4
ENSG00000237087	ENST00000836063.1	n.251-2156C>T		intron_variant	Intron 3 of 3
ECEL1P1	ENST00000373592.2	n.*59C>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32178 AN: 152014 Hom.: 4238 Cov.: 33

Gnomad AFR AF: 0.0671

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.0971

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.233

GnomAD4 exome AF: 0.230 AC: 4398 AN: 19090 Hom.: 617 AF XY: 0.235 AC XY: 2382 AN XY: 10156

African (AFR) AF: 0.0508 AC: 60 AN: 1180

American (AMR) AF: 0.182 AC: 291 AN: 1600

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 165 AN: 532

East Asian (EAS) AF: 0.0909 AC: 56 AN: 616

South Asian (SAS) AF: 0.193 AC: 411 AN: 2130

European-Finnish (FIN) AF: 0.225 AC: 170 AN: 754

Middle Eastern (MID) AF: 0.196 AC: 18 AN: 92

European-Non Finnish (NFE) AF: 0.270 AC: 2999 AN: 11124

Other (OTH) AF: 0.215 AC: 228 AN: 1062

GnomAD4 genome AF: 0.211 AC: 32170 AN: 152132 Hom.: 4240 Cov.: 33 AF XY: 0.210 AC XY: 15605 AN XY: 74380

African (AFR) AF: 0.0669 AC: 2779 AN: 41528

American (AMR) AF: 0.201 AC: 3068 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1213 AN: 3466

East Asian (EAS) AF: 0.0967 AC: 500 AN: 5170

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

European-Finnish (FIN) AF: 0.262 AC: 2775 AN: 10584

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

European-Non Finnish (NFE) AF: 0.293 AC: 19931 AN: 67974

Other (OTH) AF: 0.232 AC: 490 AN: 2114

Alfa AF: 0.241 Hom.: 1095

Bravo AF: 0.202

Asia WGS AF: 0.140 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	17
DANN	Benign	0.46
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs62192178; hg19: chr2-233280469;