22-47792504-T-C

Position:

• chr22-47792504-T-C

Variant summary

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

The NR_122046.1(EPIC1):​n.1125+53928T>C 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 0.804 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 NR_122046.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.52

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=-1.05).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPIC1	NR_122046.1	n.1125+53928T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPIC1	ENST00000651403.1	n.746+105566T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.902

Gnomad4 ASJ AF: 0.839

Gnomad4 EAS AF: 0.896

Gnomad4 SAS AF: 0.887

Gnomad4 FIN AF: 0.854

Gnomad4 NFE AF: 0.871

Gnomad4 OTH AF: 0.837

Alfa AF: 0.859 Hom.: 77149

Bravo AF: 0.801

Asia WGS AF: 0.859 AC: 2987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5767992; hg19: chr22-48188253;