rs11912108

chr22-47997675-T-G

Variant summary

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

The ENST00000651403.1(EPIC1):n.747-16066T>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 0.0666 in 152,098 control chromosomes in the GnomAD database, including 947 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 0.067 (947 hom., cov: 32)
• Consequence: EPIC1 ENST00000651403.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 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.747-16066T>G		intron_variant, non_coding_transcript_variant
EPIC1	ENST00000651033.1	n.370-16066T>G		intron_variant, non_coding_transcript_variant
EPIC1	ENST00000652228.1	n.880-16066T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0664 AC: 10098 AN: 151980 Hom.: 942 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0255

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.0699

Gnomad SAS AF: 0.00541

Gnomad FIN AF: 0.00141

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00544

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0666 AC: 10126 AN: 152098 Hom.: 947 Cov.: 32 AF XY: 0.0650 AC XY: 4833 AN XY: 74350

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.0254

Gnomad4 ASJ AF: 0.00259

Gnomad4 EAS AF: 0.0698

Gnomad4 SAS AF: 0.00520

Gnomad4 FIN AF: 0.00141

Gnomad4 NFE AF: 0.00544

Gnomad4 OTH AF: 0.0530

Alfa AF: 0.0410 Hom.: 77

Bravo AF: 0.0760

Asia WGS AF: 0.0380 AC: 131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.1
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11912108; hg19: chr22-48393424;