Genetic Variant LINC01500:n.809+11625G>C (chr14-59091401-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000654440.1(LINC01500):n.809+11625G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 152,178 control chromosomes in the GnomAD database, including 50,225 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 0.81 ( 50225 hom., cov: 31)

Consequence

LINC01500
ENST00000654440.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0760

Publications

3 publications found

Variant links:

Genes affected

LINC01500 (HGNC:51166): (long intergenic non-protein coding RNA 1500)

LINC01500 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 = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC01500	ENST00000654440.1 link	n.809+11625G>C	intron_variant	Intron 4 of 4
LINC01500	ENST00000655076.1 link	n.913+11625G>C	intron_variant	Intron 6 of 6
LINC01500	ENST00000656663.1 link	n.526-3154G>C	intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes

AF:

0.812

AC:

123445

AN:

152060

Hom.:

50179

Cov.:

show subpopulations

Gnomad AFR

AF:

0.860

Gnomad AMI

AF:

0.773

Gnomad AMR

AF:

0.819

Gnomad ASJ

AF:

0.813

Gnomad EAS

AF:

0.743

Gnomad SAS

AF:

0.759

Gnomad FIN

AF:

0.766

Gnomad MID

AF:

0.842

Gnomad NFE

AF:

0.797

Gnomad OTH

AF:

0.825

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

GnomAD4 genome

AF:

0.812

AC:

123553

AN:

152178

Hom.:

50225

Cov.:

AF XY:

0.808

AC XY:

60093

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.860

AC:

35701

AN:

41522

American (AMR)

AF:

0.819

AC:

12527

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.813

AC:

2821

AN:

3472

East Asian (EAS)

AF:

0.743

AC:

3845

AN:

5176

South Asian (SAS)

AF:

0.758

AC:

3659

AN:

4824

European-Finnish (FIN)

AF:

0.766

AC:

8102

AN:

10582

Middle Eastern (MID)

AF:

0.844

AC:

248

AN:

294

European-Non Finnish (NFE)

AF:

0.797

AC:

54205

AN:

67992

Other (OTH)

AF:

0.824

AC:

1740

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1213

2426

3639

4852

6065

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

878

1756

2634

3512

4390

<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:

0.805

Hom.:

5759

Bravo

AF:

0.820

Asia WGS

AF:

0.779

AC:

2708

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

4.8

(source)

DANN

Benign

0.54

PhyloP100

-0.076

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