dbSNP rs851426: LINC01376:n.215+12609T>A (chr2-19293214-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000418165.5(LINC01376):n.215+12609T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,986 control chromosomes in the GnomAD database, including 8,424 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 0.31 ( 8424 hom., cov: 32)

Consequence

LINC01376
ENST00000418165.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0110

Publications

3 publications found

Variant links:

Genes affected

LINC01376 (HGNC:50637): (long intergenic non-protein coding RNA 1376)

LINC01376 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01376	ENST00000418165.5 link	n.215+12609T>A	intron_variant	Intron 1 of 4	4
LINC01376	ENST00000432142.6 link	n.501+12609T>A	intron_variant	Intron 1 of 5	4
LINC01376	ENST00000449124.1 link	n.105+53430T>A	intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes

AF:

0.312

AC:

47331

AN:

151868

Hom.:

8413

Cov.:

show subpopulations

Gnomad AFR

AF:

0.501

Gnomad AMI

AF:

0.188

Gnomad AMR

AF:

0.232

Gnomad ASJ

AF:

0.300

Gnomad EAS

AF:

0.237

Gnomad SAS

AF:

0.297

Gnomad FIN

AF:

0.293

Gnomad MID

AF:

0.331

Gnomad NFE

AF:

0.227

Gnomad OTH

AF:

0.300

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

GnomAD4 genome

AF:

0.312

AC:

47385

AN:

151986

Hom.:

8424

Cov.:

AF XY:

0.312

AC XY:

23170

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.501

AC:

20759

AN:

41426

American (AMR)

AF:

0.231

AC:

3533

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.300

AC:

1041

AN:

3470

East Asian (EAS)

AF:

0.237

AC:

1229

AN:

5180

South Asian (SAS)

AF:

0.296

AC:

1424

AN:

4818

European-Finnish (FIN)

AF:

0.293

AC:

3098

AN:

10556

Middle Eastern (MID)

AF:

0.339

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.227

AC:

15408

AN:

67952

Other (OTH)

AF:

0.296

AC:

623

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1570

3139

4709

6278

7848

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

474

948

1422

1896

2370

<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:

0.268

Hom.:

789

Bravo

AF:

0.312

Asia WGS

AF:

0.235

AC:

815

AN:

3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.79

(source)

DANN

Benign

0.60

PhyloP100

-0.011

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