dbSNP rs16922670: LINC01492:n.772+2586A>G (chr9-103261938-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 ENST00000411575.5(LINC01492):n.772+2586A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,208 control chromosomes in the GnomAD database, including 2,351 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 0.16 ( 2351 hom., cov: 32)

Consequence

LINC01492
ENST00000411575.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.448

Publications

5 publications found

Variant links:

Genes affected

LINC01492 (HGNC:51149): (long intergenic non-protein coding RNA 1492)

LINC01492 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 (EAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01492	NR_121578.1 link	n.771+2586A>G		intron_variant	Intron 6 of 9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01492	ENST00000411575.5 link	n.772+2586A>G	intron_variant	Intron 6 of 9	1
LINC01492	ENST00000806271.1 link	n.415+2586A>G	intron_variant	Intron 3 of 4
LINC01492	ENST00000806272.1 link	n.550+2586A>G	intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes

AF:

0.165

AC:

25021

AN:

152090

Hom.:

2355

Cov.:

show subpopulations

Gnomad AFR

AF:

0.142

Gnomad AMI

AF:

0.203

Gnomad AMR

AF:

0.294

Gnomad ASJ

AF:

0.138

Gnomad EAS

AF:

0.332

Gnomad SAS

AF:

0.145

Gnomad FIN

AF:

0.164

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.139

Gnomad OTH

AF:

0.170

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

GnomAD4 genome

AF:

0.164

AC:

25016

AN:

152208

Hom.:

2351

Cov.:

AF XY:

0.170

AC XY:

12616

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.142

AC:

5881

AN:

41536

American (AMR)

AF:

0.294

AC:

4489

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.138

AC:

478

AN:

3468

East Asian (EAS)

AF:

0.332

AC:

1717

AN:

5166

South Asian (SAS)

AF:

0.144

AC:

696

AN:

4818

European-Finnish (FIN)

AF:

0.164

AC:

1736

AN:

10610

Middle Eastern (MID)

AF:

0.136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.139

AC:

9440

AN:

68002

Other (OTH)

AF:

0.168

AC:

354

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1058

2116

3175

4233

5291

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

268

536

804

1072

1340

<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:

0.154

Hom.:

6042

Bravo

AF:

0.176

Asia WGS

AF:

0.221

AC:

767

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

7.5

(source)

DANN

Benign

0.78

PhyloP100

-0.45

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