rs386300

Variant names:

• chr22-47714510-A-G
• rs386300
• ENST00000423737.5:n.982+9763A>G

Variant summary

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

The ENST00000423737.5(EPIC1):​n.982+9763A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,982 control chromosomes in the GnomAD database, including 10,115 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 0.34 (10115 hom., cov: 33)
• Consequence: EPIC1 ENST00000423737.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPIC1	NR_122046.1	n.982+9763A>G		intron_variant	Intron 7 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPIC1	ENST00000423737.5	n.982+9763A>G		intron_variant	Intron 7 of 8	2
EPIC1	ENST00000650660.1	n.819+27304A>G		intron_variant	Intron 6 of 6
EPIC1	ENST00000650683.1	n.1023+9763A>G		intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51811 AN: 151864 Hom.: 10099 Cov.: 33

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.341 AC: 51848 AN: 151982 Hom.: 10115 Cov.: 33 AF XY: 0.352 AC XY: 26126 AN XY: 74262

African (AFR) AF: 0.197 AC: 8163 AN: 41490

American (AMR) AF: 0.497 AC: 7602 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1083 AN: 3468

East Asian (EAS) AF: 0.673 AC: 3463 AN: 5144

South Asian (SAS) AF: 0.612 AC: 2945 AN: 4816

European-Finnish (FIN) AF: 0.359 AC: 3785 AN: 10556

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23639 AN: 67908

Other (OTH) AF: 0.361 AC: 761 AN: 2110

Alfa AF: 0.365 Hom.: 6017

Bravo AF: 0.344

Asia WGS AF: 0.601 AC: 2091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.28
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs386300; hg19: chr22-48110259;