rs7262320

chr20-18794591-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_026885.1(LCDR):n.543G>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 NR_026885.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LCDR	NR_026885.1	n.543G>T		non_coding_transcript_exon_variant	1/1
LINC00652	NR_026883.1			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LCDR	ENST00000609087.2	n.514G>T		non_coding_transcript_exon_variant	1/1
LINC00652	ENST00000664962.1			upstream_gene_variant
LINC00652	ENST00000669396.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29536 AN: 151910 Hom.: 3188 Cov.: 32

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: 4 AN: 10 Hom.: 1 Cov.: 0 AF XY: 0.400 AC XY: 4 AN XY: 10

Gnomad4 ASJ exome AF: 0.500

Gnomad4 NFE exome AF: 0.375

GnomAD4 genome AF: 0.194 AC: 29565 AN: 152028 Hom.: 3190 Cov.: 32 AF XY: 0.190 AC XY: 14131 AN XY: 74284

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.0208

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.178

Alfa AF: 0.180 Hom.: 2937

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
Dann	Benign	0.78

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7262320; hg19: chr20-18775235;