dbSNP rs2473307: 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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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