Genetic Variant ENST00000418165.5:n.351+4210A>G (chr2-19121042-T-C) – 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.351+4210A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 152,002 control chromosomes in the GnomAD database, including 26,755 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 0.59 ( 26755 hom., cov: 32)

Consequence

LINC01376
ENST00000418165.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.937

Publications

69 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 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.351+4210A>G	intron_variant	Intron 2 of 4	4
LINC01376	ENST00000432142.6 link	n.637+4210A>G	intron_variant	Intron 2 of 5	4
LINC01376	ENST00000449124.1 link	n.241+4210A>G	intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes

AF:

0.586

AC:

88960

AN:

151884

Hom.:

26732

Cov.:

show subpopulations

Gnomad AFR

AF:

0.469

Gnomad AMI

AF:

0.695

Gnomad AMR

AF:

0.671

Gnomad ASJ

AF:

0.463

Gnomad EAS

AF:

0.697

Gnomad SAS

AF:

0.424

Gnomad FIN

AF:

0.647

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.635

Gnomad OTH

AF:

0.604

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

GnomAD4 genome

AF:

0.586

AC:

89031

AN:

152002

Hom.:

26755

Cov.:

AF XY:

0.585

AC XY:

43435

AN XY:

74280

show subpopulations

African (AFR)

AF:

0.469

AC:

19460

AN:

41464

American (AMR)

AF:

0.672

AC:

10261

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.463

AC:

1606

AN:

3468

East Asian (EAS)

AF:

0.697

AC:

3595

AN:

5158

South Asian (SAS)

AF:

0.425

AC:

2042

AN:

4806

European-Finnish (FIN)

AF:

0.647

AC:

6825

AN:

10556

Middle Eastern (MID)

AF:

0.473

AC:

139

AN:

294

European-Non Finnish (NFE)

AF:

0.635

AC:

43188

AN:

67962

Other (OTH)

AF:

0.607

AC:

1281

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1832

3665

5497

7330

9162

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

744

1488

2232

2976

3720

<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:

0.619

Hom.:

64483

Bravo

AF:

0.587

Asia WGS

AF:

0.568

AC:

1974

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.7

(source)

DANN

Benign

0.51

PhyloP100

-0.94

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