Genetic Variant LINC00919:n.4A>T (chr16-52073899-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000622950.3(LINC00919):n.4A>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 0.0193 in 459,272 control chromosomes in the GnomAD database, including 133 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 0.017 ( 35 hom., cov: 33)

Exomes 𝑓: 0.020 ( 98 hom. )

Consequence

LINC00919
ENST00000622950.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.49

Publications

4 publications found

Variant links:

Genes affected

LINC00919 (HGNC:48610): (long intergenic non-protein coding RNA 919)

LINC00919 links:

LINC02911 (HGNC:44658): (long intergenic non-protein coding RNA 2911)

LINC02911 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

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02911	XR_004837540.2 link	n.299A>T	non_coding_transcript_exon_variant	Exon 3 of 8
LINC02911	XR_007065208.1 link	n.299A>T	non_coding_transcript_exon_variant	Exon 3 of 8
LINC02911	XR_007065209.1 link	n.299A>T	non_coding_transcript_exon_variant	Exon 3 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00919	ENST00000622950.3 link	n.4A>T	non_coding_transcript_exon_variant	Exon 1 of 6	2
LINC00919	ENST00000816931.1 link	n.286A>T	non_coding_transcript_exon_variant	Exon 3 of 5
LINC00919	ENST00000566314.6 link	n.286+994A>T	intron_variant	Intron 2 of 9	3

Frequencies

GnomAD3 genomes

AF:

0.0173

AC:

2626

AN:

152142

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00425

Gnomad AMI

AF:

0.0252

Gnomad AMR

AF:

0.0244

Gnomad ASJ

AF:

0.0397

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0112

Gnomad FIN

AF:

0.00443

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0256

Gnomad OTH

AF:

0.0263

GnomAD2 exomes

AF:

0.0192

AC:

2449

AN:

127442

AF XY:

0.0193

show subpopulations

Gnomad AFR exome

AF:

0.00214

Gnomad AMR exome

AF:

0.0224

Gnomad ASJ exome

AF:

0.0264

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00433

Gnomad NFE exome

AF:

0.0269

Gnomad OTH exome

AF:

0.0366

GnomAD4 exome

AF:

0.0203

AC:

6239

AN:

307012

Hom.:

Cov.:

AF XY:

0.0202

AC XY:

3532

AN XY:

174584

show subpopulations

African (AFR)

AF:

0.00564

AC:

AN:

8684

American (AMR)

AF:

0.0226

AC:

616

AN:

27198

Ashkenazi Jewish (ASJ)

AF:

0.0261

AC:

282

AN:

10792

East Asian (EAS)

AF:

0.00

AC:

AN:

9220

South Asian (SAS)

AF:

0.0110

AC:

654

AN:

59670

European-Finnish (FIN)

AF:

0.00486

AC:

AN:

12346

Middle Eastern (MID)

AF:

0.0703

AC:

195

AN:

2772

European-Non Finnish (NFE)

AF:

0.0246

AC:

3993

AN:

162022

Other (OTH)

AF:

0.0273

AC:

390

AN:

14308

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

321

642

963

1284

1605

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

104

130

<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:

0.0172

AC:

2622

AN:

152260

Hom.:

Cov.:

AF XY:

0.0162

AC XY:

1209

AN XY:

74446

show subpopulations

African (AFR)

AF:

0.00424

AC:

176

AN:

41556

American (AMR)

AF:

0.0243

AC:

372

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0397

AC:

138

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5170

South Asian (SAS)

AF:

0.0114

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.00443

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0255

AC:

1737

AN:

68012

Other (OTH)

AF:

0.0255

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

135

270

406

541

676

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

102

136

170

<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:

0.0213

Hom.:

Bravo

AF:

0.0185

Asia WGS

AF:

0.00491

AC:

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.0060

(source)

DANN

Benign

0.55

PhyloP100

-3.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

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