Genetic Variant LINC00879:n.738-16587C>T (chr3-95121599-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000462219.6(LINC00879):n.738-16587C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,150 control chromosomes in the GnomAD database, including 2,485 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 0.17 ( 2485 hom., cov: 32)

Consequence

LINC00879
ENST00000462219.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.327

Publications

5 publications found

Variant links:

Genes affected

LINC00879 (HGNC:48566): (long intergenic non-protein coding RNA 879)

LINC00879 links:

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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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.349 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
LINC00879	ENST00000462219.6 link	n.738-16587C>T	intron_variant	Intron 4 of 5	2
LINC00879	ENST00000470465.1 link	n.188-16627C>T	intron_variant	Intron 2 of 3	2
LINC00879	ENST00000651942.1 link	n.609-16587C>T	intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes

AF:

0.168

AC:

25570

AN:

152032

Hom.:

2477

Cov.:

show subpopulations

Gnomad AFR

AF:

0.197

Gnomad AMI

AF:

0.125

Gnomad AMR

AF:

0.113

Gnomad ASJ

AF:

0.129

Gnomad EAS

AF:

0.323

Gnomad SAS

AF:

0.364

Gnomad FIN

AF:

0.175

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.139

Gnomad OTH

AF:

0.163

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.168

AC:

25591

AN:

152150

Hom.:

2485

Cov.:

AF XY:

0.173

AC XY:

12830

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.197

AC:

8185

AN:

41502

American (AMR)

AF:

0.112

AC:

1720

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.129

AC:

448

AN:

3468

East Asian (EAS)

AF:

0.322

AC:

1664

AN:

5168

South Asian (SAS)

AF:

0.363

AC:

1749

AN:

4818

European-Finnish (FIN)

AF:

0.175

AC:

1852

AN:

10582

Middle Eastern (MID)

AF:

0.160

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.139

AC:

9456

AN:

68000

Other (OTH)

AF:

0.168

AC:

356

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1064

2127

3191

4254

5318

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

290

580

870

1160

1450

<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:

0.144

Hom.:

2062

Bravo

AF:

0.162

Asia WGS

AF:

0.360

AC:

1250

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.6

(source)

DANN

Benign

0.50

PhyloP100

0.33

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