dbSNP rs17718828: LINC00347:n.349-636C>T (chr13-74553977-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000594461.2(LINC00347):n.349-636C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0861 in 152,204 control chromosomes in the GnomAD database, including 602 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 0.086 ( 602 hom., cov: 32)

Exomes 𝑓: 0.25 ( 0 hom. )

Consequence

LINC00347
ENST00000594461.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.75

Publications

13 publications found

Variant links:

Genes affected

LINC00347 (HGNC:27890): (long intergenic non-protein coding RNA 347)

LINC00347 links:

LINC00402 (HGNC:42732): (long intergenic non-protein coding RNA 402)

LINC00402 links:

ENSG00000307743 (HGNC:):

ENSG00000307743 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 (NFE) allele frequency at 95% confidence interval = 0.0925 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00347	NR_034024.1 link	n.62-636C>T		intron_variant	Intron 1 of 2
LINC00347	NR_034025.1 link	n.62-680C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00347	ENST00000594461.2 link	n.349-636C>T	intron_variant	Intron 1 of 2	1
LINC00347	ENST00000601480.1 link	n.13C>T	non_coding_transcript_exon_variant	Exon 1 of 2	2
LINC00347	ENST00000451336.2 link	n.62-680C>T	intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.0859

AC:

13059

AN:

152082

Hom.:

593

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0864

Gnomad AMI

AF:

0.217

Gnomad AMR

AF:

0.0770

Gnomad ASJ

AF:

0.0903

Gnomad EAS

AF:

0.000962

Gnomad SAS

AF:

0.0286

Gnomad FIN

AF:

0.0944

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.0944

Gnomad OTH

AF:

0.0898

GnomAD4 exome

AF:

0.250

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0861

AC:

13101

AN:

152200

Hom.:

602

Cov.:

AF XY:

0.0854

AC XY:

6357

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.0871

AC:

3615

AN:

41516

American (AMR)

AF:

0.0769

AC:

1176

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0903

AC:

313

AN:

3468

East Asian (EAS)

AF:

0.000965

AC:

AN:

5184

South Asian (SAS)

AF:

0.0294

AC:

142

AN:

4822

European-Finnish (FIN)

AF:

0.0944

AC:

1000

AN:

10592

Middle Eastern (MID)

AF:

0.129

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0944

AC:

6423

AN:

68006

Other (OTH)

AF:

0.0903

AC:

191

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

605

1209

1814

2418

3023

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

140

280

420

560

700

<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:

0.0884

Hom.:

1587

Bravo

AF:

0.0835

Asia WGS

AF:

0.0270

AC:

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

0.070

(source)

DANN

Benign

0.71

PhyloP100

-1.8

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over