Genetic Variant LINC00398:n.272-8722A>G (chr13-30873838-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000690833.2(LINC00398):n.272-8722A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,238 control chromosomes in the GnomAD database, including 1,733 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 0.14 ( 1733 hom., cov: 32)

Consequence

LINC00398
ENST00000690833.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.319

Publications

2 publications found

Variant links:

Genes affected

LINC00398 (HGNC:42727): (long intergenic non-protein coding RNA 398)

LINC00398 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC00398	ENST00000690833.2 link	n.272-8722A>G	intron_variant	Intron 1 of 2
LINC00398	ENST00000715721.1 link	n.709-8722A>G	intron_variant	Intron 3 of 3
LINC00398	ENST00000799400.1 link	n.137-8722A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.141

AC:

21410

AN:

152120

Hom.:

1729

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0539

Gnomad AMI

AF:

0.114

Gnomad AMR

AF:

0.192

Gnomad ASJ

AF:

0.243

Gnomad EAS

AF:

0.269

Gnomad SAS

AF:

0.178

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.161

Gnomad OTH

AF:

0.148

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

GnomAD4 genome

AF:

0.141

AC:

21420

AN:

152238

Hom.:

1733

Cov.:

AF XY:

0.144

AC XY:

10727

AN XY:

74428

show subpopulations

African (AFR)

AF:

0.0540

AC:

2243

AN:

41556

American (AMR)

AF:

0.192

AC:

2934

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.243

AC:

845

AN:

3472

East Asian (EAS)

AF:

0.269

AC:

1389

AN:

5170

South Asian (SAS)

AF:

0.178

AC:

858

AN:

4818

European-Finnish (FIN)

AF:

0.163

AC:

1725

AN:

10592

Middle Eastern (MID)

AF:

0.160

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.161

AC:

10965

AN:

68008

Other (OTH)

AF:

0.147

AC:

310

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

966

1931

2897

3862

4828

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

240

480

720

960

1200

<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:

0.153

Hom.:

2564

Bravo

AF:

0.141

Asia WGS

AF:

0.195

AC:

681

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.5

(source)

DANN

Benign

0.51

PhyloP100

0.32

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