rs9306504

Positions:

• chr22-47851002-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.1126-3909T>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 0.0428 in 152,142 control chromosomes in the GnomAD database, including 310 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 0.043 (310 hom., cov: 32)
• Consequence: EPIC1 NR_122046.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.00

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 = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPIC1	NR_122046.1	n.1126-3909T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPIC1	ENST00000651403.1	n.747-162739T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0426 AC: 6471 AN: 152024 Hom.: 303 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0217

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.0915

Gnomad SAS AF: 0.0268

Gnomad FIN AF: 0.0192

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00907

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0428 AC: 6512 AN: 152142 Hom.: 310 Cov.: 32 AF XY: 0.0422 AC XY: 3137 AN XY: 74360

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.0217

Gnomad4 ASJ AF: 0.0170

Gnomad4 EAS AF: 0.0916

Gnomad4 SAS AF: 0.0274

Gnomad4 FIN AF: 0.0192

Gnomad4 NFE AF: 0.00907

Gnomad4 OTH AF: 0.0274

Alfa AF: 0.0240 Hom.: 27

Bravo AF: 0.0480

Asia WGS AF: 0.0410 AC: 142 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	0.012
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9306504; hg19: chr22-48246751;