dbSNP rs16882214: LNC-LBCS:n.852-46167G>C (chr6-19443704-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000636202.1(LNC-LBCS):n.852-46167G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,170 control chromosomes in the GnomAD database, including 1,555 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 0.12 ( 1555 hom., cov: 33)

Consequence

LNC-LBCS
ENST00000636202.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.08

Publications

15 publications found

Variant links:

Genes affected

LNC-LBCS (HGNC:54418): (lncRNA bladder and prostate cancer suppressor, hnRNPK interacting)

LNC-LBCS 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=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LNC-LBCS	ENST00000636202.1 link	n.852-46167G>C	intron_variant	Intron 7 of 9	5
LNC-LBCS	ENST00000653002.1 link	n.1036+91183G>C	intron_variant	Intron 8 of 8
LNC-LBCS	ENST00000660410.1 link	n.883-80880G>C	intron_variant	Intron 8 of 8

Frequencies

GnomAD3 genomes

AF:

0.123

AC:

18768

AN:

152052

Hom.:

1551

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0263

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.200

Gnomad ASJ

AF:

0.163

Gnomad EAS

AF:

0.133

Gnomad SAS

AF:

0.268

Gnomad FIN

AF:

0.214

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.139

Gnomad OTH

AF:

0.119

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

GnomAD4 genome

AF:

0.123

AC:

18782

AN:

152170

Hom.:

1555

Cov.:

AF XY:

0.132

AC XY:

9823

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.0262

AC:

1088

AN:

41528

American (AMR)

AF:

0.201

AC:

3071

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.163

AC:

566

AN:

3472

East Asian (EAS)

AF:

0.133

AC:

688

AN:

5182

South Asian (SAS)

AF:

0.267

AC:

1289

AN:

4824

European-Finnish (FIN)

AF:

0.214

AC:

2258

AN:

10574

Middle Eastern (MID)

AF:

0.0612

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.139

AC:

9431

AN:

67992

Other (OTH)

AF:

0.122

AC:

258

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

811

1623

2434

3246

4057

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

216

432

648

864

1080

<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:

0.136

Hom.:

206

Bravo

AF:

0.115

Asia WGS

AF:

0.204

AC:

709

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.17

(source)

DANN

Benign

0.78

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