Genetic Variant LNCAROD:n.123+75342C>G (chr10-52679968-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 ENST00000443523.3(LNCAROD):n.123+75342C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 151,958 control chromosomes in the GnomAD database, including 3,103 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 ( 3103 hom., cov: 32)

Consequence

LNCAROD
ENST00000443523.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.686

Publications

13 publications found

Variant links:

Genes affected

LNCAROD (HGNC:50913): (lncRNA activating regulator of DKK1)

LNCAROD links:

ENSG00000296123 (HGNC:):

ENSG00000296123 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=-0.56).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378305	NR_155748.1 link	n.95+75342C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LNCAROD	ENST00000443523.3 link	n.123+75342C>G	intron_variant	Intron 1 of 2	2
LNCAROD	ENST00000448017.3 link	n.221+75338C>G	intron_variant	Intron 1 of 2	2
LNCAROD	ENST00000647908.1 link	n.248+43902C>G	intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26473

AN:

151838

Hom.:

3089

Cov.:

show subpopulations

Gnomad AFR

AF:

0.322

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.122

Gnomad ASJ

AF:

0.0905

Gnomad EAS

AF:

0.196

Gnomad SAS

AF:

0.131

Gnomad FIN

AF:

0.155

Gnomad MID

AF:

0.0955

Gnomad NFE

AF:

0.108

Gnomad OTH

AF:

0.146

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

GnomAD4 genome

AF:

0.175

AC:

26538

AN:

151958

Hom.:

3103

Cov.:

AF XY:

0.175

AC XY:

13027

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.323

AC:

13363

AN:

41420

American (AMR)

AF:

0.122

AC:

1865

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0905

AC:

314

AN:

3468

East Asian (EAS)

AF:

0.197

AC:

1017

AN:

5172

South Asian (SAS)

AF:

0.131

AC:

631

AN:

4804

European-Finnish (FIN)

AF:

0.155

AC:

1640

AN:

10548

Middle Eastern (MID)

AF:

0.0890

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.108

AC:

7351

AN:

67952

Other (OTH)

AF:

0.150

AC:

317

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1032

2065

3097

4130

5162

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

270

540

810

1080

1350

<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:

0.145

Hom.:

272

Bravo

AF:

0.177

Asia WGS

AF:

0.192

AC:

667

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

(source)

DANN

Benign

0.59

PhyloP100

0.69

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