dbSNP rs10794359: LINC02688:n.353T>C (chr11-1051715-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 ENST00000534584.3(LINC02688):n.353T>C 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 0.575 in 152,040 control chromosomes in the GnomAD database, including 25,779 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 0.57 ( 25756 hom., cov: 32)

Exomes 𝑓: 0.59 ( 23 hom. )

Consequence

LINC02688
ENST00000534584.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.549

Publications

6 publications found

Variant links:

Genes affected

LINC02688 (HGNC:54184): (long intergenic non-protein coding RNA 2688)

LINC02688 links:

LOC124902605 (HGNC:):

LOC124902605 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 = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02688	NR_160890.1 link	n.176T>C		non_coding_transcript_exon_variant	Exon 2 of 4
LOC124902605	XM_047427955.1 link	c.-1671T>C		5_prime_UTR_variant	Exon 3 of 4		XP_047283911.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02688	ENST00000534584.3 link	n.353T>C	non_coding_transcript_exon_variant	Exon 3 of 5	3
LINC02688	ENST00000737479.1 link	n.253T>C	non_coding_transcript_exon_variant	Exon 3 of 6
LINC02688	ENST00000737480.1 link	n.191T>C	non_coding_transcript_exon_variant	Exon 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.574

AC:

87194

AN:

151802

Hom.:

25709

Cov.:

show subpopulations

Gnomad AFR

AF:

0.693

Gnomad AMI

AF:

0.518

Gnomad AMR

AF:

0.392

Gnomad ASJ

AF:

0.582

Gnomad EAS

AF:

0.566

Gnomad SAS

AF:

0.650

Gnomad FIN

AF:

0.563

Gnomad MID

AF:

0.589

Gnomad NFE

AF:

0.541

Gnomad OTH

AF:

0.559

GnomAD4 exome

AF:

0.592

AC:

AN:

120

Hom.:

Cov.:

AF XY:

0.600

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.583

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.609

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.575

AC:

87291

AN:

151920

Hom.:

25756

Cov.:

AF XY:

0.573

AC XY:

42535

AN XY:

74254

show subpopulations

African (AFR)

AF:

0.693

AC:

28728

AN:

41448

American (AMR)

AF:

0.391

AC:

5973

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.582

AC:

2017

AN:

3464

East Asian (EAS)

AF:

0.564

AC:

2906

AN:

5150

South Asian (SAS)

AF:

0.652

AC:

3135

AN:

4808

European-Finnish (FIN)

AF:

0.563

AC:

5960

AN:

10580

Middle Eastern (MID)

AF:

0.595

AC:

175

AN:

294

European-Non Finnish (NFE)

AF:

0.541

AC:

36740

AN:

67884

Other (OTH)

AF:

0.562

AC:

1186

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1860

3720

5579

7439

9299

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

756

1512

2268

3024

3780

<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:

0.545

Hom.:

28318

Bravo

AF:

0.566

Asia WGS

AF:

0.599

AC:

2086

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

5.1

(source)

DANN

Benign

0.77

PhyloP100

0.55

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