Genetic Variant LINC00917:n.1705G>C (chr16-86347578-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000598994.3(LINC00917):n.1705G>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 0.203 in 152,424 control chromosomes in the GnomAD database, including 3,354 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 0.20 ( 3351 hom., cov: 33)

Exomes 𝑓: 0.19 ( 3 hom. )

Consequence

LINC00917
ENST00000598994.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.133

Publications

10 publications found

Variant links:

Genes affected

LINC00917 (HGNC:48607): (long intergenic non-protein coding RNA 917)

LINC00917 links:

ENSG00000269826 (HGNC:):

ENSG00000269826 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 (SAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00917	ENST00000598994.3 link	n.1705G>C	non_coding_transcript_exon_variant	Exon 2 of 2	2
LINC00917	ENST00000595169.6 link	n.89+1973G>C	intron_variant	Intron 1 of 5	2
ENSG00000269826	ENST00000595705.1 link	n.63+129C>G	intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.203

AC:

30859

AN:

152102

Hom.:

3349

Cov.:

show subpopulations

Gnomad AFR

AF:

0.161

Gnomad AMI

AF:

0.185

Gnomad AMR

AF:

0.263

Gnomad ASJ

AF:

0.174

Gnomad EAS

AF:

0.277

Gnomad SAS

AF:

0.329

Gnomad FIN

AF:

0.130

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.213

Gnomad OTH

AF:

0.217

GnomAD4 exome

AF:

0.191

AC:

AN:

204

Hom.:

AF XY:

0.182

AC XY:

AN XY:

148

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.211

AC:

AN:

166

Other (OTH)

AF:

0.0714

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.203

AC:

30861

AN:

152220

Hom.:

3351

Cov.:

AF XY:

0.204

AC XY:

15163

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.160

AC:

6661

AN:

41526

American (AMR)

AF:

0.263

AC:

4021

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.174

AC:

604

AN:

3470

East Asian (EAS)

AF:

0.277

AC:

1431

AN:

5168

South Asian (SAS)

AF:

0.330

AC:

1592

AN:

4828

European-Finnish (FIN)

AF:

0.130

AC:

1379

AN:

10616

Middle Eastern (MID)

AF:

0.248

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.213

AC:

14476

AN:

68008

Other (OTH)

AF:

0.216

AC:

456

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1263

2525

3788

5050

6313

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

344

688

1032

1376

1720

<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:

0.114

Hom.:

204

Bravo

AF:

0.212

Asia WGS

AF:

0.269

AC:

936

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

5.9

(source)

DANN

Benign

0.54

PhyloP100

0.13

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