dbSNP rs9321637: LINC02865:n.101+82T>C (chr6-137945548-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 ENST00000417800.1(LINC02865):n.101+82T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,388 control chromosomes in the GnomAD database, including 2,777 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 0.17 ( 2776 hom., cov: 31)

Exomes 𝑓: 0.076 ( 1 hom. )

Consequence

LINC02865
ENST00000417800.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

Publications

14 publications found

Variant links:

Genes affected

LINC02865 (HGNC:54516): (long intergenic non-protein coding RNA 2865)

LINC02865 links:

SIMALR (HGNC:53554): (suppressor of inflammatory macrophage apoptosis lncRNA)

SIMALR 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=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SIMALR	NR_149097.1 link	n.132+121A>G		intron_variant	Intron 1 of 1
LINC02865	NR_174953.1 link	n.119+82T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02865	ENST00000417800.1 link	n.101+82T>C	intron_variant	Intron 1 of 1	2
SIMALR	ENST00000417932.2 link	n.355+121A>G	intron_variant	Intron 3 of 3	3
LINC02865	ENST00000434437.5 link	n.101+82T>C	intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes

AF:

0.166

AC:

25208

AN:

152086

Hom.:

2776

Cov.:

show subpopulations

Gnomad AFR

AF:

0.317

Gnomad AMI

AF:

0.115

Gnomad AMR

AF:

0.0943

Gnomad ASJ

AF:

0.103

Gnomad EAS

AF:

0.0235

Gnomad SAS

AF:

0.0782

Gnomad FIN

AF:

0.123

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.118

Gnomad OTH

AF:

0.145

GnomAD4 exome

AF:

0.0761

AC:

AN:

184

Hom.:

Cov.:

AF XY:

0.0556

AC XY:

AN XY:

108

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.0580

AC:

AN:

138

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.136

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.417

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.166

AC:

25221

AN:

152204

Hom.:

2776

Cov.:

AF XY:

0.162

AC XY:

12071

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.316

AC:

13112

AN:

41492

American (AMR)

AF:

0.0942

AC:

1442

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.103

AC:

356

AN:

3470

East Asian (EAS)

AF:

0.0235

AC:

122

AN:

5182

South Asian (SAS)

AF:

0.0783

AC:

378

AN:

4828

European-Finnish (FIN)

AF:

0.123

AC:

1304

AN:

10616

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.118

AC:

8055

AN:

67998

Other (OTH)

AF:

0.144

AC:

304

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1005

2010

3016

4021

5026

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

254

508

762

1016

1270

<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:

0.138

Hom.:

4119

Bravo

AF:

0.168

Asia WGS

AF:

0.0570

AC:

201

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

4.2

(source)

DANN

Benign

0.52

PhyloP100

0.0

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over