dbSNP rs17085106: LINC01899:n.244+10353C>A (chr18-71771837-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000583756.2(LINC01899):n.244+10353C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0603 in 150,276 control chromosomes in the GnomAD database, including 612 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 0.060 ( 612 hom., cov: 33)

Consequence

LINC01899
ENST00000583756.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0460

Publications

12 publications found

Variant links:

Genes affected

LINC01899 (HGNC:52718): (long intergenic non-protein coding RNA 1899)

LINC01899 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01899	NR_126324.1 link	n.37+10353C>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01899	ENST00000583756.2 link	n.244+10353C>A	intron_variant	Intron 3 of 6	3
LINC01899	ENST00000764766.1 link	n.168+10353C>A	intron_variant	Intron 2 of 4
LINC01899	ENST00000764767.1 link	n.240+10353C>A	intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.0602

AC:

9036

AN:

150156

Hom.:

612

Cov.:

show subpopulations

Gnomad AFR

AF:

0.170

Gnomad AMI

AF:

0.00442

Gnomad AMR

AF:

0.0311

Gnomad ASJ

AF:

0.0257

Gnomad EAS

AF:

0.000401

Gnomad SAS

AF:

0.0458

Gnomad FIN

AF:

0.0102

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0166

Gnomad OTH

AF:

0.0596

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

GnomAD4 genome

AF:

0.0603

AC:

9062

AN:

150276

Hom.:

612

Cov.:

AF XY:

0.0586

AC XY:

4294

AN XY:

73294

show subpopulations

African (AFR)

AF:

0.170

AC:

6934

AN:

40852

American (AMR)

AF:

0.0310

AC:

461

AN:

14866

Ashkenazi Jewish (ASJ)

AF:

0.0257

AC:

AN:

3466

East Asian (EAS)

AF:

0.000402

AC:

AN:

4978

South Asian (SAS)

AF:

0.0463

AC:

218

AN:

4710

European-Finnish (FIN)

AF:

0.0102

AC:

107

AN:

10458

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0166

AC:

1123

AN:

67680

Other (OTH)

AF:

0.0585

AC:

121

AN:

2068

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

402

804

1205

1607

2009

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:

0.0299

Hom.:

772

Bravo

AF:

0.0653

Asia WGS

AF:

0.0320

AC:

110

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.8

(source)

DANN

Benign

0.27

PhyloP100

-0.046

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