22-47875964-A-T

Position:

• chr22-47875964-A-T

Variant summary

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

The ENST00000651403.1(EPIC1):​n.747-137777A>T 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 0.219 in 151,778 control chromosomes in the GnomAD database, including 4,092 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 0.22 (4092 hom., cov: 33)
• Consequence: EPIC1 ENST00000651403.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EPIC1	ENST00000651403.1	n.747-137777A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33281 AN: 151660 Hom.: 4088 Cov.: 33

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.219 AC: 33297 AN: 151778 Hom.: 4092 Cov.: 33 AF XY: 0.221 AC XY: 16414 AN XY: 74130

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.217

Alfa AF: 0.224 Hom.: 528

Bravo AF: 0.214

Asia WGS AF: 0.366 AC: 1265 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs728591; hg19: chr22-48271713;