rs1884516

Positions:

• 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 ENST00000651403.1(EPIC1):​n.747-83966A>G variant causes a intron, non coding transcript 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 ENST00000651403.1 intron, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPIC1	ENST00000651403.1	n.747-83966A>G		intron_variant, non_coding_transcript_variant

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;