rs9306504

Variant names:

• chr22-47851002-T-C
• rs9306504
• ENST00000423737.5:n.1126-3909T>C

Variant summary

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

The ENST00000423737.5(EPIC1):​n.1126-3909T>C variant causes a intron 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 ENST00000423737.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.00
• Publications: 0 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.108 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.1126-3909T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPIC1	ENST00000423737.5	TSL:2	n.1126-3909T>C		intron	N/A
	EPIC1	ENST00000650660.1		n.820-77742T>C		intron	N/A
	EPIC1	ENST00000650683.1		n.1024-77742T>C		intron	N/A

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

African (AFR) AF: 0.111 AC: 4588 AN: 41488

American (AMR) AF: 0.0217 AC: 332 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0170 AC: 59 AN: 3472

East Asian (EAS) AF: 0.0916 AC: 473 AN: 5166

South Asian (SAS) AF: 0.0274 AC: 132 AN: 4818

European-Finnish (FIN) AF: 0.0192 AC: 203 AN: 10582

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00907 AC: 617 AN: 68006

Other (OTH) AF: 0.0274 AC: 58 AN: 2114

Alfa AF: 0.0459 Hom.: 146

Bravo AF: 0.0480

Asia WGS AF: 0.0410 AC: 142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.012
DANN	Benign	0.55
PhyloP100		-4.0

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: rs9306504;

hg19: chr22-48246751;