dbSNP rs11003107: LNCAROD:n.123+7743G>A (chr10-52747567-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 ENST00000443523.3(LNCAROD):n.123+7743G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0367 in 152,154 control chromosomes in the GnomAD database, including 240 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 0.037 ( 240 hom., cov: 33)

Consequence

LNCAROD
ENST00000443523.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.482

Publications

1 publications found

Variant links:

Genes affected

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

LNCAROD links:

LOC105378305 (HGNC:):

LOC105378305 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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378305	NR_155748.1 link	n.95+7743G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LNCAROD	ENST00000443523.3 link	n.123+7743G>A	intron_variant	Intron 1 of 2	2
LNCAROD	ENST00000448017.3 link	n.221+7739G>A	intron_variant	Intron 1 of 2	2
LNCAROD	ENST00000647908.1 link	n.99+7739G>A	intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes

AF:

0.0367

AC:

5575

AN:

152036

Hom.:

240

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0927

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0324

Gnomad ASJ

AF:

0.00634

Gnomad EAS

AF:

0.136

Gnomad SAS

AF:

0.00976

Gnomad FIN

AF:

0.0270

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00168

Gnomad OTH

AF:

0.0330

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

GnomAD4 genome

AF:

0.0367

AC:

5580

AN:

152154

Hom.:

240

Cov.:

AF XY:

0.0376

AC XY:

2794

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.0928

AC:

3849

AN:

41490

American (AMR)

AF:

0.0323

AC:

493

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.00634

AC:

AN:

3472

East Asian (EAS)

AF:

0.135

AC:

700

AN:

5172

South Asian (SAS)

AF:

0.00956

AC:

AN:

4812

European-Finnish (FIN)

AF:

0.0270

AC:

286

AN:

10596

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00168

AC:

114

AN:

68012

Other (OTH)

AF:

0.0322

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

254

508

762

1016

1270

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

192

256

320

<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:

0.0132

Hom.:

Bravo

AF:

0.0419

Asia WGS

AF:

0.0520

AC:

179

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.4

(source)

DANN

Benign

0.44

PhyloP100

-0.48

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