dbSNP rs13114426: LINC01365:n.273-536G>A (chr4-119801930-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 ENST00000503266.6(LINC01365):n.273-536G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,944 control chromosomes in the GnomAD database, including 8,084 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 0.31 ( 8084 hom., cov: 31)

Consequence

LINC01365
ENST00000503266.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0790

Publications

3 publications found

Variant links:

Genes affected

LINC01365 (HGNC:50603): (long intergenic non-protein coding RNA 1365)

LINC01365 links:

ENSG00000300267 (HGNC:):

ENSG00000300267 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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01365	NR_110660.2 link	n.236-536G>A		intron_variant	Intron 2 of 4
LINC01365	NR_174111.1 link	n.235+794G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01365	ENST00000503266.6 link	n.273-536G>A	intron_variant	Intron 2 of 4	1
LINC01365	ENST00000512219.1 link	n.218+794G>A	intron_variant	Intron 2 of 4	5
LINC01365	ENST00000669300.2 link	n.239+794G>A	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.306

AC:

46451

AN:

151826

Hom.:

8084

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.441

Gnomad AMR

AF:

0.281

Gnomad ASJ

AF:

0.400

Gnomad EAS

AF:

0.335

Gnomad SAS

AF:

0.244

Gnomad FIN

AF:

0.373

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.400

Gnomad OTH

AF:

0.291

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

GnomAD4 genome

AF:

0.306

AC:

46452

AN:

151944

Hom.:

8084

Cov.:

AF XY:

0.304

AC XY:

22588

AN XY:

74256

show subpopulations

African (AFR)

AF:

0.137

AC:

5679

AN:

41452

American (AMR)

AF:

0.281

AC:

4291

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.400

AC:

1387

AN:

3470

East Asian (EAS)

AF:

0.335

AC:

1725

AN:

5148

South Asian (SAS)

AF:

0.244

AC:

1173

AN:

4808

European-Finnish (FIN)

AF:

0.373

AC:

3932

AN:

10548

Middle Eastern (MID)

AF:

0.310

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.400

AC:

27162

AN:

67944

Other (OTH)

AF:

0.289

AC:

611

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1571

3142

4714

6285

7856

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

464

928

1392

1856

2320

<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:

0.329

Hom.:

1498

Bravo

AF:

0.292

Asia WGS

AF:

0.240

AC:

838

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.5

(source)

DANN

Benign

0.73

PhyloP100

-0.079

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