Genetic Variant LRRC52-AS1:n.1443-1805A>G (chr1-165478920-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000416424.5(LRRC52-AS1):n.1443-1805A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 151,812 control chromosomes in the GnomAD database, including 11,723 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 0.38 ( 11723 hom., cov: 30)

Consequence

LRRC52-AS1
ENST00000416424.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.12

Publications

5 publications found

Variant links:

Genes affected

LRRC52-AS1 (HGNC:54044): (LRRC52 antisense RNA 1)

LRRC52-AS1 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=-0.7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC52-AS1	NR_026744.2 link	n.1530-1805A>G		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LRRC52-AS1	ENST00000416424.5 link	n.1443-1805A>G	intron_variant	Intron 5 of 5	1
LRRC52-AS1	ENST00000415000.3 link	n.554-1805A>G	intron_variant	Intron 2 of 2	3
LRRC52-AS1	ENST00000421273.5 link	n.1479-1805A>G	intron_variant	Intron 6 of 6	2

Frequencies

GnomAD3 genomes

AF:

0.377

AC:

57213

AN:

151694

Hom.:

11728

Cov.:

show subpopulations

Gnomad AFR

AF:

0.258

Gnomad AMI

AF:

0.367

Gnomad AMR

AF:

0.451

Gnomad ASJ

AF:

0.437

Gnomad EAS

AF:

0.816

Gnomad SAS

AF:

0.472

Gnomad FIN

AF:

0.321

Gnomad MID

AF:

0.462

Gnomad NFE

AF:

0.398

Gnomad OTH

AF:

0.405

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

GnomAD4 genome

AF:

0.377

AC:

57232

AN:

151812

Hom.:

11723

Cov.:

AF XY:

0.379

AC XY:

28080

AN XY:

74184

show subpopulations

African (AFR)

AF:

0.257

AC:

10644

AN:

41394

American (AMR)

AF:

0.451

AC:

6890

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.437

AC:

1515

AN:

3464

East Asian (EAS)

AF:

0.815

AC:

4199

AN:

5152

South Asian (SAS)

AF:

0.471

AC:

2257

AN:

4788

European-Finnish (FIN)

AF:

0.321

AC:

3373

AN:

10504

Middle Eastern (MID)

AF:

0.473

AC:

139

AN:

294

European-Non Finnish (NFE)

AF:

0.398

AC:

27023

AN:

67926

Other (OTH)

AF:

0.408

AC:

859

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1685

3369

5054

6738

8423

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

558

1116

1674

2232

2790

<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:

0.399

Hom.:

52544

Bravo

AF:

0.384

Asia WGS

AF:

0.613

AC:

2134

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

(source)

DANN

Benign

0.95

PhyloP100

1.1

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