20-18795391-G-A

Variant names:

• chr20-18795391-G-A
• rs80046336
• ENST00000609087.2:n.1314G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000609087.2(LCDR):​n.1314G>A 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 0.144 in 145,798 control chromosomes in the GnomAD database, including 1,760 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 0.14 (1759 hom., cov: 33)
  • Exomes 𝑓: 0.40 (1 hom.)
• Consequence: LCDR ENST00000609087.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LCDR	NR_026885.1	n.1343G>A		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LCDR	ENST00000609087.2	n.1314G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
LCDR	ENST00000740308.1	n.890G>A		non_coding_transcript_exon_variant	Exon 2 of 2
LCDR	ENST00000740309.1	n.617G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.144 AC: 20924 AN: 145676 Hom.: 1758 Cov.: 33

Gnomad AFR AF: 0.0508

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0729

Gnomad EAS AF: 0.0861

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.0929

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.123

GnomAD4 exome AF: 0.400 AC: 4 AN: 10 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 3 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

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: 0.400 AC: 4 AN: 10

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.144 AC: 20931 AN: 145788 Hom.: 1759 Cov.: 33 AF XY: 0.147 AC XY: 10469 AN XY: 71296

African (AFR) AF: 0.0509 AC: 1945 AN: 38242

American (AMR) AF: 0.117 AC: 1746 AN: 14930

Ashkenazi Jewish (ASJ) AF: 0.0729 AC: 250 AN: 3428

East Asian (EAS) AF: 0.0853 AC: 441 AN: 5170

South Asian (SAS) AF: 0.206 AC: 968 AN: 4694

European-Finnish (FIN) AF: 0.236 AC: 2404 AN: 10190

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 290

European-Non Finnish (NFE) AF: 0.192 AC: 12675 AN: 65932

Other (OTH) AF: 0.122 AC: 246 AN: 2020

Alfa AF: 0.0962 Hom.: 157

Bravo AF: 0.124

Asia WGS AF: 0.129 AC: 449 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.66
DANN	Benign	0.64
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs80046336; hg19: chr20-18776035;