Genetic Variant LINC02665:n.610G>T (chr10-7097556-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 ENST00000420049.3(LINC02665):n.610G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0679 in 152,260 control chromosomes in the GnomAD database, including 908 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 0.068 ( 908 hom., cov: 33)

Exomes 𝑓: 0.15 ( 0 hom. )

Consequence

LINC02665
ENST00000420049.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.682

Publications

1 publications found

Variant links:

Genes affected

LINC02665 (HGNC:54151): (long intergenic non-protein coding RNA 2665)

LINC02665 links:

ENSG00000287277 (HGNC:):

ENSG00000287277 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02665	NR_184104.1 link	n.534G>T		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105376387	NR_188183.1 link	n.190+20724C>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02665	ENST00000420049.3 link	n.610G>T	non_coding_transcript_exon_variant	Exon 3 of 3	3
LINC02665	ENST00000830756.1 link	n.505G>T	non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000287277	ENST00000664549.1 link	n.190+20724C>A	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.0680

AC:

10342

AN:

152122

Hom.:

914

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0615

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.113

Gnomad ASJ

AF:

0.0608

Gnomad EAS

AF:

0.474

Gnomad SAS

AF:

0.127

Gnomad FIN

AF:

0.0226

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0346

Gnomad OTH

AF:

0.0761

GnomAD4 exome

AF:

0.150

AC:

AN:

Hom.:

Cov.:

AF XY:

0.143

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0833

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.675

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0679

AC:

10343

AN:

152240

Hom.:

908

Cov.:

AF XY:

0.0712

AC XY:

5301

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.0617

AC:

2564

AN:

41530

American (AMR)

AF:

0.113

AC:

1729

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0608

AC:

211

AN:

3472

East Asian (EAS)

AF:

0.474

AC:

2447

AN:

5162

South Asian (SAS)

AF:

0.126

AC:

611

AN:

4832

European-Finnish (FIN)

AF:

0.0226

AC:

240

AN:

10604

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0346

AC:

2356

AN:

68022

Other (OTH)

AF:

0.0753

AC:

159

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

459

918

1377

1836

2295

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

240

360

480

600

<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:

0.0293

Hom.:

Bravo

AF:

0.0755

Asia WGS

AF:

0.277

AC:

961

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.22

(source)

DANN

Benign

0.77

PhyloP100

-0.68

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