dbSNP rs6008359: EPIC1:n.983-1595C>T (chr22-47736839-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000423737.5(EPIC1):n.983-1595C>T variant causes a intron 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
ENST00000423737.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.522

Publications

2 publications found

Variant links:

Genes affected

EPIC1 (HGNC:27672): (epigenetically induced MYC interacting lncRNA 1)

EPIC1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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 = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPIC1	NR_122046.1 link	n.983-1595C>T		intron_variant	Intron 7 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
EPIC1	ENST00000423737.5 link	n.983-1595C>T	intron_variant	Intron 7 of 8	2
EPIC1	ENST00000650660.1 link	n.819+49633C>T	intron_variant	Intron 6 of 6
EPIC1	ENST00000650683.1 link	n.1023+32092C>T	intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes

AF:

0.302

AC:

45937

AN:

151950

Hom.:

7659

Cov.:

show subpopulations

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.:

AF XY:

0.299

AC XY:

22207

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.456

AC:

18897

AN:

41474

American (AMR)

AF:

0.225

AC:

3446

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.311

AC:

1080

AN:

3468

East Asian (EAS)

AF:

0.208

AC:

1075

AN:

5156

South Asian (SAS)

AF:

0.268

AC:

1293

AN:

4818

European-Finnish (FIN)

AF:

0.206

AC:

2184

AN:

10580

Middle Eastern (MID)

AF:

0.274

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.253

AC:

17165

AN:

67968

Other (OTH)

AF:

0.287

AC:

606

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1551

3101

4652

6202

7753

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

454

908

1362

1816

2270

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.272

Hom.:

17293

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

(source)

DANN

Benign

0.58

PhyloP100

-0.52

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over