dbSNP rs6576507: LINC02346:n.896-5878T>C (chr15-26043247-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 ENST00000383019.2(LINC02346):n.896-5878T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0424 in 152,236 control chromosomes in the GnomAD database, including 458 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 0.042 ( 458 hom., cov: 33)

Consequence

LINC02346
ENST00000383019.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.114

Publications

8 publications found

Variant links:

Genes affected

LINC02346 (HGNC:53268): (long intergenic non-protein coding RNA 2346)

LINC02346 links:

ENSG00000306598 (HGNC:):

ENSG00000306598 links:

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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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02346	NR_040082.1 link	n.896-5878T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02346	ENST00000383019.2 link	n.896-5878T>C	intron_variant	Intron 2 of 4	2
LINC02346	ENST00000659028.1 link	n.404-8781T>C	intron_variant	Intron 1 of 2
LINC02346	ENST00000659702.1 link	n.627-8781T>C	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0423

AC:

6428

AN:

152118

Hom.:

449

Cov.:

show subpopulations

Gnomad AFR

AF:

0.146

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0194

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.000367

Gnomad OTH

AF:

0.0302

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

GnomAD4 genome

AF:

0.0424

AC:

6461

AN:

152236

Hom.:

458

Cov.:

AF XY:

0.0407

AC XY:

3029

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.146

AC:

6070

AN:

41504

American (AMR)

AF:

0.0193

AC:

295

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5186

South Asian (SAS)

AF:

0.00124

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10612

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000367

AC:

AN:

68034

Other (OTH)

AF:

0.0299

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

280

560

839

1119

1399

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0152

Hom.:

338

Bravo

AF:

0.0473

Asia WGS

AF:

0.0100

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.99

(source)

DANN

Benign

0.43

PhyloP100

-0.11

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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rs6576507

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