dbSNP rs7262320: LCDR:n.514G>T (chr20-18794591-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000609087.2(LCDR):n.514G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,038 control chromosomes in the GnomAD database, including 3,191 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 0.19 ( 3190 hom., cov: 32)

Exomes 𝑓: 0.40 ( 1 hom. )

Consequence

LCDR
ENST00000609087.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0800

Publications

10 publications found

Variant links:

Genes affected

LCDR (HGNC:44308): (lysosome cell death regulator)

LCDR links:

LINC00652 (HGNC:25003): (long intergenic non-protein coding RNA 652)

LINC00652 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=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LCDR	NR_026885.1 link	n.543G>T		non_coding_transcript_exon_variant	Exon 1 of 1
LINC00652	NR_026883.1 link	n.-7C>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LCDR	ENST00000609087.2 link	n.514G>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
LCDR	ENST00000740308.1 link	n.90G>T	non_coding_transcript_exon_variant	Exon 2 of 2
LCDR	ENST00000740309.1 link	n.30-213G>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.194

AC:

29536

AN:

151910

Hom.:

3188

Cov.:

show subpopulations

Gnomad AFR

AF:

0.267

Gnomad AMI

AF:

0.154

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.114

Gnomad EAS

AF:

0.0211

Gnomad SAS

AF:

0.134

Gnomad FIN

AF:

0.193

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.185

Gnomad OTH

AF:

0.180

GnomAD4 exome

AF:

0.400

AC:

AN:

Hom.:

Cov.:

AF XY:

0.400

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.375

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.600

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.194

AC:

29565

AN:

152028

Hom.:

3190

Cov.:

AF XY:

0.190

AC XY:

14131

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.267

AC:

11051

AN:

41442

American (AMR)

AF:

0.145

AC:

2222

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.114

AC:

394

AN:

3466

East Asian (EAS)

AF:

0.0208

AC:

107

AN:

5156

South Asian (SAS)

AF:

0.134

AC:

646

AN:

4820

European-Finnish (FIN)

AF:

0.193

AC:

2033

AN:

10560

Middle Eastern (MID)

AF:

0.133

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.185

AC:

12558

AN:

67984

Other (OTH)

AF:

0.178

AC:

375

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1184

2369

3553

4738

5922

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

308

616

924

1232

1540

<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:

0.188

Hom.:

5548

Bravo

AF:

0.195

Asia WGS

AF:

0.0940

AC:

327

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

8.0

(source)

DANN

Benign

0.78

PhyloP100

-0.080

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