Genetic Variant ENSG00000294899:n.342-1373_342-1372insGGG (chr2-127133887-T-TGGG) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000726607.1(ENSG00000294899):n.342-1373_342-1372insGGG variant causes a intron 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 0.30 ( 7024 hom., cov: 0)

Consequence

ENSG00000294899
ENST00000726607.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.396

Publications

21 publications found

Variant links:

Genes affected

ENSG00000294899 (HGNC:):

ENSG00000294899 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726607.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294899	ENST00000726607.1		n.342-1373_342-1372insGGG		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.301

AC:

45400

AN:

150912

Hom.:

6994

Cov.:

show subpopulations

Gnomad AFR

AF:

0.349

Gnomad AMI

AF:

0.294

Gnomad AMR

AF:

0.335

Gnomad ASJ

AF:

0.301

Gnomad EAS

AF:

0.333

Gnomad SAS

AF:

0.212

Gnomad FIN

AF:

0.235

Gnomad MID

AF:

0.229

Gnomad NFE

AF:

0.279

Gnomad OTH

AF:

0.287

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

GnomAD4 genome

AF:

0.301

AC:

45478

AN:

151028

Hom.:

7024

Cov.:

AF XY:

0.298

AC XY:

21973

AN XY:

73774

show subpopulations

African (AFR)

AF:

0.349

AC:

14329

AN:

41066

American (AMR)

AF:

0.336

AC:

5103

AN:

15184

Ashkenazi Jewish (ASJ)

AF:

0.301

AC:

1041

AN:

3458

East Asian (EAS)

AF:

0.334

AC:

1709

AN:

5124

South Asian (SAS)

AF:

0.212

AC:

1014

AN:

4788

European-Finnish (FIN)

AF:

0.235

AC:

2446

AN:

10410

Middle Eastern (MID)

AF:

0.229

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.279

AC:

18889

AN:

67712

Other (OTH)

AF:

0.294

AC:

614

AN:

2088

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

1492

2984

4477

5969

7461

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

446

892

1338

1784

2230

<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:

0.121

Hom.:

194

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.40

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over