Variant 22-47687480-A-AAGGTCCG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NR_122046.1(EPIC1):n.823+277_823+278insTCCGAGG variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 1.0 ( 75528 hom., cov: 0)

Consequence

EPIC1
NR_122046.1 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.194

Variant links:

Genes affected

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

EPIC1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EPIC1	NR_122046.1 linkuse as main transcript	n.823+277_823+278insTCCGAGG		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EPIC1	ENST00000651403.1 linkuse as main transcript	n.746+545_746+546insTCCGAGG		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.996

AC:

151521

AN:

152100

Hom.:

75472

Cov.:

show subpopulations

Gnomad AFR

AF:

0.987

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.999

Gnomad ASJ

AF:

1.00

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.999

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

1.00

Gnomad NFE

AF:

1.00

Gnomad OTH

AF:

0.995

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

GnomAD4 genome

AF:

0.996

AC:

151636

AN:

152218

Hom.:

75528

Cov.:

AF XY:

0.996

AC XY:

74144

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.987

Gnomad4 AMR

AF:

0.999

Gnomad4 ASJ

AF:

1.00

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.999

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

1.00

Gnomad4 OTH

AF:

0.995

Alfa

AF:

1.00

Hom.:

2235

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over