dbSNP rs2723603: LINC02743:n.121+10585C>T (chr11-133799492-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 ENST00000526254.1(LINC02743):n.121+10585C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,180 control chromosomes in the GnomAD database, including 945 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 0.10 ( 945 hom., cov: 33)

Consequence

LINC02743
ENST00000526254.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.276

Publications

1 publications found

Variant links:

Genes affected

LINC02743 (HGNC:54261): (long intergenic non-protein coding RNA 2743)

LINC02743 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=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02743	NR_120444.1 link	n.121+10585C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02743	ENST00000526254.1 link	n.121+10585C>T	intron_variant	Intron 2 of 2	5
LINC02743	ENST00000762255.1 link	n.263+10585C>T	intron_variant	Intron 2 of 6
LINC02743	ENST00000762256.1 link	n.273+10585C>T	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15655

AN:

152062

Hom.:

942

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.0866

Gnomad AMR

AF:

0.100

Gnomad ASJ

AF:

0.0842

Gnomad EAS

AF:

0.231

Gnomad SAS

AF:

0.134

Gnomad FIN

AF:

0.0529

Gnomad MID

AF:

0.134

Gnomad NFE

AF:

0.0872

Gnomad OTH

AF:

0.109

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

GnomAD4 genome

AF:

0.103

AC:

15680

AN:

152180

Hom.:

945

Cov.:

AF XY:

0.102

AC XY:

7583

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.125

AC:

5180

AN:

41498

American (AMR)

AF:

0.100

AC:

1529

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0842

AC:

292

AN:

3468

East Asian (EAS)

AF:

0.231

AC:

1196

AN:

5170

South Asian (SAS)

AF:

0.134

AC:

644

AN:

4822

European-Finnish (FIN)

AF:

0.0529

AC:

560

AN:

10592

Middle Eastern (MID)

AF:

0.134

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0872

AC:

5932

AN:

68018

Other (OTH)

AF:

0.108

AC:

229

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

739

1477

2216

2954

3693

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

368

552

736

920

<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:

0.0948

Hom.:

2400

Bravo

AF:

0.108

Asia WGS

AF:

0.185

AC:

645

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

3.4

(source)

DANN

Benign

0.74

PhyloP100

0.28

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