Genetic Variant ENST00000423311.1:n.512+7228_512+7229insT (chr22-35164206-C-CA) – ACMG Classification: Benign (-8 pts)

Variant summary

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

The ENST00000423311.1(LINC01399):n.512+7228_512+7229insT 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 0.34 ( 7968 hom., cov: 0)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

LINC01399
ENST00000423311.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.226

Publications

3 publications found

Variant links:

Genes affected

LINC01399 (HGNC:):

LINC01399 links:

LINC01399 (HGNC:50680): (long intergenic non-protein coding RNA 1399)

LINC01399 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000423311.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000423311.1. 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
	LINC01399	NR_126356.1		n.512+7228dupT		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
LINC01399	ENST00000423311.1	TSL:3	n.512+7228_512+7229insT	intron	N/A
LINC01399	ENST00000798716.1		n.352+7228_352+7229insT	intron	N/A
ENSG00000238153	ENST00000414048.1	TSL:6	n.-98_-97insA	upstream_gene	N/A

Frequencies

GnomAD3 genomes

AF:

0.336

AC:

38981

AN:

115914

Hom.:

7959

Cov.:

show subpopulations

Gnomad AFR

AF:

0.546

Gnomad AMI

AF:

0.182

Gnomad AMR

AF:

0.295

Gnomad ASJ

AF:

0.232

Gnomad EAS

AF:

0.602

Gnomad SAS

AF:

0.370

Gnomad FIN

AF:

0.244

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.228

Gnomad OTH

AF:

0.328

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

AF XY:

0.00

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.336

AC:

38982

AN:

115888

Hom.:

7968

Cov.:

AF XY:

0.341

AC XY:

18297

AN XY:

53598

show subpopulations

African (AFR)

AF:

0.547

AC:

16659

AN:

30480

American (AMR)

AF:

0.295

AC:

3025

AN:

10264

Ashkenazi Jewish (ASJ)

AF:

0.232

AC:

711

AN:

3064

East Asian (EAS)

AF:

0.603

AC:

2415

AN:

4006

South Asian (SAS)

AF:

0.369

AC:

1171

AN:

3172

European-Finnish (FIN)

AF:

0.244

AC:

955

AN:

3920

Middle Eastern (MID)

AF:

0.298

AC:

AN:

238

European-Non Finnish (NFE)

AF:

0.228

AC:

13327

AN:

58406

Other (OTH)

AF:

0.329

AC:

498

AN:

1514

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1039

2078

3116

4155

5194

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

368

736

1104

1472

1840

<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:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.23

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.

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