Genetic Variant LINC01399:n.353-21117G>T (chr22-35097374-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000798716.1(LINC01399):n.353-21117G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,252 control chromosomes in the GnomAD database, including 2,403 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 0.10 ( 2403 hom., cov: 33)

Consequence

LINC01399
ENST00000798716.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0870

Publications

2 publications found

Variant links:

Genes affected

LINC01399 (HGNC:):

LINC01399 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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01399	ENST00000798716.1 link	n.353-21117G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.100

AC:

15262

AN:

152136

Hom.:

2391

Cov.:

show subpopulations

Gnomad AFR

AF:

0.336

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0357

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.0402

Gnomad SAS

AF:

0.0354

Gnomad FIN

AF:

0.00960

Gnomad MID

AF:

0.0191

Gnomad NFE

AF:

0.00237

Gnomad OTH

AF:

0.0688

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

GnomAD4 genome

AF:

0.101

AC:

15319

AN:

152252

Hom.:

2403

Cov.:

AF XY:

0.0974

AC XY:

7252

AN XY:

74444

show subpopulations

African (AFR)

AF:

0.337

AC:

13977

AN:

41498

American (AMR)

AF:

0.0355

AC:

544

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.000576

AC:

AN:

3470

East Asian (EAS)

AF:

0.0401

AC:

208

AN:

5184

South Asian (SAS)

AF:

0.0353

AC:

170

AN:

4822

European-Finnish (FIN)

AF:

0.00960

AC:

102

AN:

10624

Middle Eastern (MID)

AF:

0.0205

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.00237

AC:

161

AN:

68030

Other (OTH)

AF:

0.0691

AC:

146

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

532

1064

1595

2127

2659

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

276

414

552

690

<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:

0.0322

Hom.:

762

Bravo

AF:

0.112

Asia WGS

AF:

0.0810

AC:

284

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.82

(source)

DANN

Benign

0.42

PhyloP100

-0.087

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