dbSNP rs2660753: LINC00506:n.508+19817T>C (chr3-87061524-T-C) – ACMG Classification: Benign (-12 pts)

Germline classification Cancer classification (beta)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BA1BP4_Strong

The ENST00000774840.1(LINC00506):n.508+19817T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a cumulative frequency of 0.761 (AC=115,728) in the gnomAD database across 152,054 control chromosomes, including 46,501 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.882. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.76 ( 46501 hom., cov: 31)

Consequence

LINC00506
ENST00000774840.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.15

Publications

143 publications found

Variant links:

Genes affected

LINC00506 (HGNC:43557): (long intergenic non-protein coding RNA 506)

LINC00506 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000774840.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).

BA1

GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.8816 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000774840.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00506	ENST00000774840.1		n.508+19817T>C		intron	N/A
	LINC00506	ENST00000774841.1		n.454+19817T>C		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.761

AC:

115690

AN:

151936

Hom.:

46491

Cov.:

show subpopulations

Gnomad AFR

AF:

0.486

Gnomad AMI

AF:

0.889

Gnomad AMR

AF:

0.825

Gnomad ASJ

AF:

0.779

Gnomad EAS

AF:

0.743

Gnomad SAS

AF:

0.763

Gnomad FIN

AF:

0.926

Gnomad MID

AF:

0.725

Gnomad NFE

AF:

0.888

Gnomad OTH

AF:

0.775

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

GnomAD4 genome

AF:

0.761

AC:

115728

AN:

152054

Hom.:

46501

Cov.:

AF XY:

0.762

AC XY:

56658

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.485

AC:

20095

AN:

41420

American (AMR)

AF:

0.825

AC:

12604

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.779

AC:

2702

AN:

3470

East Asian (EAS)

AF:

0.743

AC:

3839

AN:

5170

South Asian (SAS)

AF:

0.763

AC:

3678

AN:

4818

European-Finnish (FIN)

AF:

0.926

AC:

9822

AN:

10606

Middle Eastern (MID)

AF:

0.721

AC:

212

AN:

294

European-Non Finnish (NFE)

AF:

0.888

AC:

60330

AN:

67974

Other (OTH)

AF:

0.777

AC:

1637

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1164

2328

3492

4656

5820

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

832

1664

2496

3328

4160

<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:

0.840

Hom.:

199642

Bravo

AF:

0.741

Asia WGS

AF:

0.717

AC:

2494

AN:

3476

Local populations

ToMMo 61KJPN (+60KJPN MNV)

AF:

0.731

AC:

89318

AN:

122200

Turkish Variome

AF:

0.793

AC:

1226

AN:

1546

Hom.:

487

WBBC (Westlake BioBank for Chinese) pilot

AF:

0.736

AC:

6593

AN:

8960

Hom.:

2439

ABraOM SABE-WGS-1171

AF:

0.768

AC:

1799

AN:

2342

Hom.:

710

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

7.2

(source)

DANN

Benign

0.37

PhyloP100

1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Local populations

ClinVar

Computational scores

Splicing

Publications

Other links and lift over