Genetic Variant LINC01705:n.635-25260G>A (chr1-221865713-C-T) – 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 XR_007066885.1(LOC124904517):n.330+13648C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a cumulative frequency of 0.457 (AC=69,385) in the gnomAD database across 151,988 control chromosomes, including 16,202 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.613. 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 0.46 ( 16202 hom., cov: 32)

Consequence

LOC124904517
XR_007066885.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.476

Publications

4 publications found

Variant links:

Genes affected

LINC01705 (HGNC:52493): (long intergenic non-protein coding RNA 1705)

LINC01705 links:

ENSG00000307440 (HGNC:):

ENSG00000307440 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript XR_007066885.1, 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 = 0.6130 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715677.1. 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

Gene	Transcript	HGVSc	Effect	Exon Rank
LINC01705	ENST00000715677.1	n.635-25260G>A	intron	N/A
LINC01705	ENST00000826165.1	n.477-25260G>A	intron	N/A
LINC01705	ENST00000826167.1	n.470-25260G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.457

AC:

69354

AN:

151870

Hom.:

16201

Cov.:

show subpopulations

Gnomad AFR

AF:

0.463

Gnomad AMI

AF:

0.353

Gnomad AMR

AF:

0.571

Gnomad ASJ

AF:

0.513

Gnomad EAS

AF:

0.631

Gnomad SAS

AF:

0.467

Gnomad FIN

AF:

0.430

Gnomad MID

AF:

0.541

Gnomad NFE

AF:

0.415

Gnomad OTH

AF:

0.465

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

GnomAD4 genome

AF:

0.457

AC:

69385

AN:

151988

Hom.:

16202

Cov.:

AF XY:

0.461

AC XY:

34237

AN XY:

74296

show subpopulations

African (AFR)

AF:

0.462

AC:

19163

AN:

41438

American (AMR)

AF:

0.572

AC:

8732

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.513

AC:

1782

AN:

3472

East Asian (EAS)

AF:

0.631

AC:

3265

AN:

5174

South Asian (SAS)

AF:

0.466

AC:

2244

AN:

4818

European-Finnish (FIN)

AF:

0.430

AC:

4539

AN:

10548

Middle Eastern (MID)

AF:

0.538

AC:

157

AN:

292

European-Non Finnish (NFE)

AF:

0.415

AC:

28195

AN:

67950

Other (OTH)

AF:

0.468

AC:

987

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1925

3849

5774

7698

9623

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

628

1256

1884

2512

3140

<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:

0.438

Hom.:

46946

Bravo

AF:

0.472

Asia WGS

AF:

0.590

AC:

2050

AN:

3478

Local populations

ToMMo 61KJPN (+60KJPN MNV)

AF:

0.619

AC:

75998

AN:

122818

Turkish Variome

AF:

0.457

AC:

706

AN:

1546

Hom.:

166

WBBC (Westlake BioBank for Chinese) pilot

AF:

0.642

AC:

5750

AN:

8960

Hom.:

1889

ABraOM SABE-WGS-1171

AF:

0.488

AC:

1142

AN:

2342

Hom.:

276

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.3

(source)

DANN

Benign

0.73

PhyloP100

-0.48

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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