Genetic Variant LINC01635:n.351A>G (chr1-22024341-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 ENST00000455966.2(LINC01635):n.351A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 152,112 control chromosomes in the GnomAD database, including 23,703 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 0.55 ( 23696 hom., cov: 32)

Exomes 𝑓: 0.55 ( 7 hom. )

Consequence

LINC01635
ENST00000455966.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.338

Publications

12 publications found

Variant links:

Genes affected

LINC01635 (HGNC:52422): (long intergenic non-protein coding RNA 1635)

LINC01635 links:

ENSG00000285959 (HGNC:):

ENSG00000285959 links:

LINC00339 (HGNC:25011): (long intergenic non-protein coding RNA 339)

LINC00339 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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01635	NR_110692.1 link	n.351A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01635	ENST00000455966.2 link	n.351A>G	non_coding_transcript_exon_variant	Exon 3 of 3	1
LINC01635	ENST00000635097.3 link	n.688A>G	non_coding_transcript_exon_variant	Exon 3 of 3	5
LINC01635	ENST00000655353.1 link	n.688A>G	non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.549

AC:

83339

AN:

151930

Hom.:

23660

Cov.:

show subpopulations

Gnomad AFR

AF:

0.684

Gnomad AMI

AF:

0.207

Gnomad AMR

AF:

0.422

Gnomad ASJ

AF:

0.591

Gnomad EAS

AF:

0.366

Gnomad SAS

AF:

0.605

Gnomad FIN

AF:

0.450

Gnomad MID

AF:

0.497

Gnomad NFE

AF:

0.522

Gnomad OTH

AF:

0.568

GnomAD4 exome

AF:

0.548

AC:

AN:

Hom.:

Cov.:

AF XY:

0.587

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.520

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.549

AC:

83428

AN:

152050

Hom.:

23696

Cov.:

AF XY:

0.542

AC XY:

40281

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.684

AC:

28360

AN:

41478

American (AMR)

AF:

0.422

AC:

6434

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.591

AC:

2052

AN:

3470

East Asian (EAS)

AF:

0.367

AC:

1900

AN:

5180

South Asian (SAS)

AF:

0.604

AC:

2914

AN:

4828

European-Finnish (FIN)

AF:

0.450

AC:

4764

AN:

10580

Middle Eastern (MID)

AF:

0.500

AC:

146

AN:

292

European-Non Finnish (NFE)

AF:

0.522

AC:

35463

AN:

67952

Other (OTH)

AF:

0.572

AC:

1207

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1893

3785

5678

7570

9463

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

720

1440

2160

2880

3600

<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:

0.527

Hom.:

7598

Bravo

AF:

0.548

Asia WGS

AF:

0.538

AC:

1872

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.1

(source)

DANN

Benign

0.77

PhyloP100

-0.34

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over