Genetic Variant LINC00163:n.183+93G>T (chr21-44993811-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000434081.1(LINC00163):n.183+93G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 147,684 control chromosomes in the GnomAD database, including 2,624 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 0.19 ( 2592 hom., cov: 32)

Exomes 𝑓: 0.060 ( 32 hom. )

Consequence

LINC00163
ENST00000434081.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.43

Publications

1 publications found

Variant links:

Genes affected

LINC00163 (HGNC:33165): (long intergenic non-protein coding RNA 163)

LINC00163 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=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00163	NR_033840.1 link	n.183+93G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00163	ENST00000434081.1 link	n.183+93G>T		intron_variant	Intron 1 of 1	1
LINC00163	ENST00000439088.1 link	n.166+93G>T		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes

AF:

0.189

AC:

27222

AN:

143968

Hom.:

2592

Cov.:

show subpopulations

Gnomad AFR

AF:

0.152

Gnomad AMI

AF:

0.200

Gnomad AMR

AF:

0.245

Gnomad ASJ

AF:

0.239

Gnomad EAS

AF:

0.169

Gnomad SAS

AF:

0.116

Gnomad FIN

AF:

0.178

Gnomad MID

AF:

0.132

Gnomad NFE

AF:

0.202

Gnomad OTH

AF:

0.181

GnomAD4 exome

AF:

0.0601

AC:

218

AN:

3626

Hom.:

AF XY:

0.0649

AC XY:

151

AN XY:

2326

show subpopulations

African (AFR)

AF:

0.0313

AC:

AN:

American (AMR)

AF:

0.125

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.0625

AC:

AN:

East Asian (EAS)

AF:

0.0278

AC:

AN:

South Asian (SAS)

AF:

0.0236

AC:

AN:

974

European-Finnish (FIN)

AF:

0.00917

AC:

AN:

218

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0832

AC:

175

AN:

2104

Other (OTH)

AF:

0.0604

AC:

AN:

182

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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:

0.189

AC:

27229

AN:

144058

Hom.:

2592

Cov.:

AF XY:

0.188

AC XY:

13307

AN XY:

70710

show subpopulations

African (AFR)

AF:

0.152

AC:

5207

AN:

34312

American (AMR)

AF:

0.245

AC:

3665

AN:

14942

Ashkenazi Jewish (ASJ)

AF:

0.239

AC:

828

AN:

3458

East Asian (EAS)

AF:

0.169

AC:

864

AN:

5118

South Asian (SAS)

AF:

0.116

AC:

555

AN:

4794

European-Finnish (FIN)

AF:

0.178

AC:

1869

AN:

10508

Middle Eastern (MID)

AF:

0.122

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.202

AC:

13652

AN:

67704

Other (OTH)

AF:

0.184

AC:

373

AN:

2030

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1068

2136

3203

4271

5339

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

292

584

876

1168

1460

<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:

0.193

Hom.:

858

Bravo

AF:

0.187

Asia WGS

AF:

0.158

AC:

548

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.3

(source)

DANN

Benign

0.57

PhyloP100

-1.4

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