dbSNP rs7085203: LINC02667:n.-138C>T (chr10-128912659-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000446589.2(LINC02667):n.-138C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,160 control chromosomes in the GnomAD database, including 1,527 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 0.14 ( 1527 hom., cov: 33)

Consequence

LINC02667
ENST00000446589.2 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.47

Publications

8 publications found

Variant links:

Genes affected

LINC02667 (HGNC:54153): (long intergenic non-protein coding RNA 2667)

LINC02667 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.22).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02667	NR_148990.1 link	n.-174C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
LINC02667	ENST00000446589.2 link	n.-138C>T	upstream_gene_variant	2
LINC02667	ENST00000656262.2 link	n.-150C>T	upstream_gene_variant
LINC02667	ENST00000661127.1 link	n.-157C>T	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.139

AC:

21106

AN:

152042

Hom.:

1525

Cov.:

show subpopulations

Gnomad AFR

AF:

0.160

Gnomad AMI

AF:

0.0965

Gnomad AMR

AF:

0.117

Gnomad ASJ

AF:

0.103

Gnomad EAS

AF:

0.146

Gnomad SAS

AF:

0.142

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.138

Gnomad OTH

AF:

0.166

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

GnomAD4 genome

AF:

0.139

AC:

21117

AN:

152160

Hom.:

1527

Cov.:

AF XY:

0.138

AC XY:

10284

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.160

AC:

6629

AN:

41492

American (AMR)

AF:

0.117

AC:

1787

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.103

AC:

356

AN:

3472

East Asian (EAS)

AF:

0.145

AC:

751

AN:

5168

South Asian (SAS)

AF:

0.142

AC:

683

AN:

4826

European-Finnish (FIN)

AF:

0.101

AC:

1071

AN:

10590

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.138

AC:

9353

AN:

68010

Other (OTH)

AF:

0.165

AC:

349

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

931

1861

2792

3722

4653

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

232

464

696

928

1160

<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:

0.139

Hom.:

6543

Bravo

AF:

0.139

Asia WGS

AF:

0.126

AC:

439

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.22

CADD

Benign

(source)

DANN

Benign

0.72

PhyloP100

1.5

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over