chr2-232378254-G-A

Variant names:

• chr2-232378254-G-A
• rs2014683
• ENST00000715297.1:n.812+691C>T

Variant summary

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

The ENST00000715297.1(ECEL1P2):​n.812+691C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,938 control chromosomes in the GnomAD database, including 15,146 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 0.44 (15146 hom., cov: 32)
• Consequence: ECEL1P2 ENST00000715297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 7 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124906123	XR_007088121.1	n.88+691C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ECEL1P2	ENST00000715297.1	n.812+691C>T		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66602 AN: 151820 Hom.: 15133 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.439 AC: 66629 AN: 151938 Hom.: 15146 Cov.: 32 AF XY: 0.445 AC XY: 33064 AN XY: 74274

African (AFR) AF: 0.329 AC: 13634 AN: 41442

American (AMR) AF: 0.531 AC: 8111 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1745 AN: 3468

East Asian (EAS) AF: 0.606 AC: 3114 AN: 5142

South Asian (SAS) AF: 0.535 AC: 2579 AN: 4820

European-Finnish (FIN) AF: 0.547 AC: 5792 AN: 10584

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.446 AC: 30287 AN: 67898

Other (OTH) AF: 0.440 AC: 926 AN: 2106

Alfa AF: 0.455 Hom.: 13672

Bravo AF: 0.436

Asia WGS AF: 0.594 AC: 2061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.1
DANN	Benign	0.69
PhyloP100		0.059
PromoterAI		-0.026	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2014683; hg19: chr2-233242964;