rs386300

chr22-47714510-A-G

Variant summary

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

The NR_122046.1(EPIC1):n.982+9763A>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 0.341 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 NR_122046.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

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=-0.98).
• 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/exons	MANE	UniProt
EPIC1	NR_122046.1	n.982+9763A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPIC1	ENST00000651403.1	n.746+27572A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.361

Alfa AF: 0.368 Hom.: 5513

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs386300; hg19: chr22-48110259;