Genetic Variant LINC01399:n.512+7228_512+7229insTT (chr22-35164206-C-CAA) – ACMG Classification: Benign (-8 pts)

Variant summary

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

The ENST00000423311.1(LINC01399):n.512+7228_512+7229insTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 115,624 control chromosomes in the GnomAD database, including 20,533 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.54 ( 20533 hom., cov: 0)

Exomes 𝑓: 0.30 ( 0 hom. )

Consequence

LINC01399
ENST00000423311.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.226

Variant links:

Genes affected

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

LINC01399 links:

ENSG00000238153 (HGNC:):

ENSG00000238153 links:

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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 = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01399	NR_126356.1 link	n.512+7227_512+7228dupTT		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01399	ENST00000423311.1 link	n.512+7228_512+7229insTT		intron_variant	Intron 4 of 5	3
ENSG00000238153	ENST00000414048.1 link	n.-98_-97insAA		upstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.545

AC:

63045

AN:

115642

Hom.:

20547

Cov.:

show subpopulations

Gnomad AFR

AF:

0.183

Gnomad AMI

AF:

0.729

Gnomad AMR

AF:

0.627

Gnomad ASJ

AF:

0.707

Gnomad EAS

AF:

0.389

Gnomad SAS

AF:

0.569

Gnomad FIN

AF:

0.657

Gnomad MID

AF:

0.591

Gnomad NFE

AF:

0.710

Gnomad OTH

AF:

0.572

GnomAD4 exome

AF:

0.300

AC:

AN:

Hom.:

AF XY:

0.300

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.375

GnomAD4 genome

AF:

0.545

AC:

63006

AN:

115614

Hom.:

20533

Cov.:

AF XY:

0.538

AC XY:

28797

AN XY:

53488

show subpopulations

Gnomad4 AFR

AF:

0.183

Gnomad4 AMR

AF:

0.627

Gnomad4 ASJ

AF:

0.707

Gnomad4 EAS

AF:

0.388

Gnomad4 SAS

AF:

0.570

Gnomad4 FIN

AF:

0.657

Gnomad4 NFE

AF:

0.710

Gnomad4 OTH

AF:

0.572

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.

22-35164206-CAAAAA-CAAAAAAA

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