rs1884516

Variant names:

• chr22-47929775-A-G
• rs1884516
• ENST00000651003.1:n.771-17791A>G

Your query was ambiguous. Multiple possible variants found:

• chr22-47929775-A-G
• chr22-47929775-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651003.1(EPIC1):​n.771-17791A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,212 control chromosomes in the GnomAD database, including 1,270 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 0.13 (1270 hom., cov: 33)
• Consequence: EPIC1 ENST00000651003.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518

Genes affected

EPIC1 (HGNC:27672): (epigenetically induced MYC interacting lncRNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.179 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
EPIC1	ENST00000651003.1	n.771-17791A>G		intron_variant	Intron 6 of 6
EPIC1	ENST00000651033.1	n.370-83966A>G		intron_variant	Intron 4 of 6
EPIC1	ENST00000651124.1	n.907-17791A>G		intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19074 AN: 152094 Hom.: 1271 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0935

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.125 AC: 19082 AN: 152212 Hom.: 1270 Cov.: 33 AF XY: 0.128 AC XY: 9549 AN XY: 74432

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.0934

Gnomad4 OTH AF: 0.133

Alfa AF: 0.105 Hom.: 1199

Bravo AF: 0.133

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.20
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1884516; hg19: chr22-48325524;