2-232378127-T-C

Variant names:

• chr2-232378127-T-C
• rs3762524
• ENST00000715297.1:n.812+818A>G

Variant summary

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

The ENST00000715297.1(ECEL1P2):​n.812+818A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,126 control chromosomes in the GnomAD database, including 18,739 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 0.49 (18739 hom., cov: 34)
• Consequence: ECEL1P2 ENST00000715297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 3 publications found

Genes affected

ECEL1P2 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715297.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ECEL1P2	ENST00000715297.1		n.812+818A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.487 AC: 74076 AN: 152006 Hom.: 18716 Cov.: 34

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.493

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.487 AC: 74127 AN: 152126 Hom.: 18739 Cov.: 34 AF XY: 0.494 AC XY: 36733 AN XY: 74372

African (AFR) AF: 0.353 AC: 14634 AN: 41502

American (AMR) AF: 0.583 AC: 8911 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1846 AN: 3472

East Asian (EAS) AF: 0.617 AC: 3182 AN: 5158

South Asian (SAS) AF: 0.608 AC: 2934 AN: 4822

European-Finnish (FIN) AF: 0.602 AC: 6389 AN: 10616

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34720 AN: 67958

Other (OTH) AF: 0.497 AC: 1048 AN: 2108

Alfa AF: 0.501 Hom.: 9460

Bravo AF: 0.482

Asia WGS AF: 0.653 AC: 2269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.43
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs3762524; hg19: chr2-233242837;