Genetic Variant ENST00000420049.3: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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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