dbSNP rs11260603: LINC01342:n.1382T>C (chr1-1143818-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 ENST00000416774.1(LINC01342):n.1382T>C 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 0.332 in 151,972 control chromosomes in the GnomAD database, including 10,135 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 0.33 ( 10126 hom., cov: 33)

Exomes 𝑓: 0.24 ( 9 hom. )

Consequence

LINC01342
ENST00000416774.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.69

Publications

7 publications found

Variant links:

Genes affected

LINC01342 (HGNC:50551): (long intergenic non-protein coding RNA 1342)

LINC01342 links:

LOC124903820 (HGNC:):

LOC124903820 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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01342	NR_038869.1 link	n.1382T>C		non_coding_transcript_exon_variant	Exon 3 of 3
LOC124903820	XR_007065351.1 link	n.76-14664T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01342	ENST00000416774.1 link	n.1382T>C		non_coding_transcript_exon_variant	Exon 3 of 3	1

Frequencies

GnomAD3 genomes

AF:

0.332

AC:

50334

AN:

151620

Hom.:

10095

Cov.:

show subpopulations

Gnomad AFR

AF:

0.565

Gnomad AMI

AF:

0.236

Gnomad AMR

AF:

0.185

Gnomad ASJ

AF:

0.195

Gnomad EAS

AF:

0.0465

Gnomad SAS

AF:

0.281

Gnomad FIN

AF:

0.333

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.259

Gnomad OTH

AF:

0.270

GnomAD4 exome

AF:

0.237

AC:

AN:

236

Hom.:

Cov.:

AF XY:

0.247

AC XY:

AN XY:

186

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.400

AC:

AN:

European-Finnish (FIN)

AF:

0.375

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.215

AC:

AN:

186

Other (OTH)

AF:

0.350

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.332

AC:

50413

AN:

151736

Hom.:

10126

Cov.:

AF XY:

0.331

AC XY:

24582

AN XY:

74166

show subpopulations

African (AFR)

AF:

0.565

AC:

23348

AN:

41296

American (AMR)

AF:

0.185

AC:

2823

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.195

AC:

675

AN:

3462

East Asian (EAS)

AF:

0.0462

AC:

239

AN:

5174

South Asian (SAS)

AF:

0.281

AC:

1356

AN:

4826

European-Finnish (FIN)

AF:

0.333

AC:

3514

AN:

10540

Middle Eastern (MID)

AF:

0.286

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.259

AC:

17601

AN:

67882

Other (OTH)

AF:

0.267

AC:

560

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1580

3160

4739

6319

7899

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

478

956

1434

1912

2390

<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:

0.282

Hom.:

12857

Bravo

AF:

0.329

Asia WGS

AF:

0.167

AC:

578

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.15

(source)

DANN

Benign

0.30

PhyloP100

-2.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

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