dbSNP rs2118381: LINC01376:n.216-42930C>T (chr2-19168317-G-A) – 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.216-42930C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 152,098 control chromosomes in the GnomAD database, including 35,149 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 0.67 ( 35149 hom., cov: 34)

Consequence

LINC01376
ENST00000418165.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0780

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=-0.96).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.757 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.216-42930C>T	intron_variant	Intron 1 of 4	4
LINC01376	ENST00000432142.6 link	n.502-42930C>T	intron_variant	Intron 1 of 5	4
LINC01376	ENST00000449124.1 link	n.106-42930C>T	intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes

AF:

0.669

AC:

101643

AN:

151980

Hom.:

35138

Cov.:

show subpopulations

Gnomad AFR

AF:

0.482

Gnomad AMI

AF:

0.627

Gnomad AMR

AF:

0.689

Gnomad ASJ

AF:

0.607

Gnomad EAS

AF:

0.680

Gnomad SAS

AF:

0.714

Gnomad FIN

AF:

0.764

Gnomad MID

AF:

0.612

Gnomad NFE

AF:

0.763

Gnomad OTH

AF:

0.671

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

GnomAD4 genome

AF:

0.669

AC:

101678

AN:

152098

Hom.:

35149

Cov.:

AF XY:

0.669

AC XY:

49766

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.481

AC:

19962

AN:

41460

American (AMR)

AF:

0.689

AC:

10524

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.607

AC:

2106

AN:

3472

East Asian (EAS)

AF:

0.680

AC:

3512

AN:

5168

South Asian (SAS)

AF:

0.715

AC:

3453

AN:

4826

European-Finnish (FIN)

AF:

0.764

AC:

8089

AN:

10590

Middle Eastern (MID)

AF:

0.603

AC:

175

AN:

290

European-Non Finnish (NFE)

AF:

0.763

AC:

51863

AN:

67990

Other (OTH)

AF:

0.673

AC:

1422

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1690

3381

5071

6762

8452

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

806

1612

2418

3224

4030

<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:

0.726

Hom.:

125103

Bravo

AF:

0.651

Asia WGS

AF:

0.717

AC:

2485

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.71

(source)

DANN

Benign

0.61

PhyloP100

-0.078

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