rs6008359

chr22-47736839-C-T

Variant summary

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

The NR_122046.1(EPIC1):n.983-1595C>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 0.302 in 152,068 control chromosomes in the GnomAD database, including 7,667 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 0.30 (7667 hom., cov: 32)
• Consequence: EPIC1 NR_122046.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522

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 (AFR) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPIC1	NR_122046.1	n.983-1595C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPIC1	ENST00000651403.1	n.746+49901C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45937 AN: 151950 Hom.: 7659 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.302 AC: 45967 AN: 152068 Hom.: 7667 Cov.: 32 AF XY: 0.299 AC XY: 22207 AN XY: 74334

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.287

Alfa AF: 0.264 Hom.: 6022

Bravo AF: 0.309

Asia WGS AF: 0.267 AC: 931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.0
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6008359; hg19: chr22-48132588;