rs7262320

Variant names:

• chr20-18794591-G-T
• rs7262320
• ENST00000609087.2:n.514G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

Genes affected

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

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

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_026885.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LCDR	NR_026885.1		n.543G>T		non_coding_transcript_exon	Exon 1 of 1
	LINC00652	NR_026883.1		n.-7C>A		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LCDR	ENST00000609087.2	TSL:6	n.514G>T		non_coding_transcript_exon	Exon 1 of 1
	LCDR	ENST00000740308.1		n.90G>T		non_coding_transcript_exon	Exon 2 of 2
	LCDR	ENST00000740309.1		n.30-213G>T		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.375 AC: 3 AN: 8

Other (OTH) AC: 0 AN: 0

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

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: 39 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12558 AN: 67984

Other (OTH) AF: 0.178 AC: 375 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.0
DANN	Benign	0.78
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs7262320; hg19: chr20-18775235;