rs10052280

Variant names:

• chr5-84601266-A-G
• rs10052280
• ENST00000846037.1:n.406-598A>G

Variant summary

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

The ENST00000846037.1(EDIL3-DT):​n.406-598A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 149,738 control chromosomes in the GnomAD database, including 1,444 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 0.11 (1444 hom., cov: 27)
• Consequence: EDIL3-DT ENST00000846037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 1 publications found

Genes affected

EDIL3-DT (HGNC:40204): (EDIL3 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 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
EDIL3-DT	ENST00000846037.1	n.406-598A>G		intron_variant	Intron 4 of 5
EDIL3-DT	ENST00000846038.1	n.331-598A>G		intron_variant	Intron 3 of 4
EDIL3-DT	ENST00000846040.1	n.166-598A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17183 AN: 149708 Hom.: 1437 Cov.: 27

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.0859

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0707

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0304

Gnomad FIN AF: 0.0686

Gnomad MID AF: 0.0523

Gnomad NFE AF: 0.0559

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.115 AC: 17212 AN: 149738 Hom.: 1444 Cov.: 27 AF XY: 0.116 AC XY: 8505 AN XY: 73054

African (AFR) AF: 0.222 AC: 9094 AN: 40908

American (AMR) AF: 0.153 AC: 2286 AN: 14986

Ashkenazi Jewish (ASJ) AF: 0.0707 AC: 245 AN: 3466

East Asian (EAS) AF: 0.135 AC: 687 AN: 5104

South Asian (SAS) AF: 0.0306 AC: 146 AN: 4776

European-Finnish (FIN) AF: 0.0686 AC: 660 AN: 9626

Middle Eastern (MID) AF: 0.0571 AC: 16 AN: 280

European-Non Finnish (NFE) AF: 0.0559 AC: 3779 AN: 67620

Other (OTH) AF: 0.107 AC: 221 AN: 2064

Alfa AF: 0.0723 Hom.: 2329

Bravo AF: 0.127

Asia WGS AF: 0.100 AC: 347 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.66
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs10052280; hg19: chr5-83897084;