chr2-232418305-A-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836067.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000237087	ENST00000836067.1		n.789T>A		non_coding_transcript_exon	Exon 4 of 5
	ENSG00000237087	ENST00000836080.1		n.383T>A		non_coding_transcript_exon	Exon 2 of 3
	ECEL1P1	ENST00000373592.2	TSL:6	n.852-14T>A		intron	N/A

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 v4.9

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;