chr22-47792504-T-C

Variant names:

• chr22-47792504-T-C
• rs5767992
• ENST00000423737.5:n.1125+53928T>C

Variant summary

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

The ENST00000423737.5(EPIC1):​n.1125+53928T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 152,122 control chromosomes in the GnomAD database, including 50,284 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 0.80 (50284 hom., cov: 32)
• Consequence: EPIC1 ENST00000423737.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.52
• Publications: 7 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=-1.05).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000423737.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPIC1	NR_122046.1		n.1125+53928T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPIC1	ENST00000423737.5	TSL:2	n.1125+53928T>C		intron	N/A
	EPIC1	ENST00000650660.1		n.819+105298T>C		intron	N/A
	EPIC1	ENST00000650683.1		n.1023+87757T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122245 AN: 152004 Hom.: 50257 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.804 AC: 122316 AN: 152122 Hom.: 50284 Cov.: 32 AF XY: 0.807 AC XY: 59975 AN XY: 74356

African (AFR) AF: 0.618 AC: 25628 AN: 41450

American (AMR) AF: 0.902 AC: 13789 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.839 AC: 2914 AN: 3472

East Asian (EAS) AF: 0.896 AC: 4631 AN: 5168

South Asian (SAS) AF: 0.887 AC: 4270 AN: 4816

European-Finnish (FIN) AF: 0.854 AC: 9047 AN: 10594

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.871 AC: 59257 AN: 68014

Other (OTH) AF: 0.837 AC: 1769 AN: 2114

Alfa AF: 0.846 Hom.: 175277

Bravo AF: 0.801

Asia WGS AF: 0.859 AC: 2987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.39
DANN	Benign	0.19
PhyloP100		-3.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5767992;

hg19: chr22-48188253;