dbSNP rs7593687: LINC01320:n.475+89679C>T (chr2-34474248-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 ENST00000422558.1(LINC01320):n.475+89679C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0758 in 133,852 control chromosomes in the GnomAD database, including 1,700 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 0.076 ( 1700 hom., cov: 23)

Consequence

LINC01320
ENST00000422558.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.40

Publications

1 publications found

Variant links:

Genes affected

LINC01320 (HGNC:50526): (long intergenic non-protein coding RNA 1320)

LINC01320 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01320	ENST00000422558.1 link	n.475+89679C>T	intron_variant	Intron 2 of 2	4
LINC01320	ENST00000650021.1 link	n.219+89679C>T	intron_variant	Intron 4 of 6
LINC01320	ENST00000654103.1 link	n.532-2316C>T	intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.0758

AC:

10141

AN:

133740

Hom.:

1698

Cov.:

show subpopulations

Gnomad AFR

AF:

0.235

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0367

Gnomad ASJ

AF:

0.00233

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000680

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0219

Gnomad NFE

AF:

0.00153

Gnomad OTH

AF:

0.0600

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

GnomAD4 genome

AF:

0.0758

AC:

10152

AN:

133852

Hom.:

1700

Cov.:

AF XY:

0.0737

AC XY:

4795

AN XY:

65074

show subpopulations

African (AFR)

AF:

0.234

AC:

9481

AN:

40436

American (AMR)

AF:

0.0366

AC:

463

AN:

12656

Ashkenazi Jewish (ASJ)

AF:

0.00233

AC:

AN:

3000

East Asian (EAS)

AF:

0.00

AC:

AN:

5140

South Asian (SAS)

AF:

0.000455

AC:

AN:

4398

European-Finnish (FIN)

AF:

0.00

AC:

AN:

8308

Middle Eastern (MID)

AF:

0.0236

AC:

AN:

254

European-Non Finnish (NFE)

AF:

0.00153

AC:

AN:

57336

Other (OTH)

AF:

0.0593

AC:

105

AN:

1772

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

335

671

1006

1342

1677

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

276

368

460

<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:

0.0594

Hom.:

123

Asia WGS

AF:

0.0110

AC:

AN:

3378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.96

(source)

DANN

Benign

0.75

PhyloP100

-1.4

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