rs41309831

chr20-18794220-C-T

Variant summary

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

The NR_026883.1(LINC00652):n.365G>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 0.132 in 152,164 control chromosomes in the GnomAD database, including 1,446 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 0.13 (1446 hom., cov: 32)
  • Exomes 𝑓: 0.086 (0 hom.)
• Consequence: LINC00652 NR_026883.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00652	NR_026883.1	n.365G>A		non_coding_transcript_exon_variant	1/4
LCDR	NR_026885.1	n.172C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LCDR	ENST00000609087.2	n.143C>T		non_coding_transcript_exon_variant	1/1
LINC00652	ENST00000664962.1	n.355G>A		non_coding_transcript_exon_variant	1/4

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20136 AN: 151976 Hom.: 1446 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0211

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.130

GnomAD4 exome AF: 0.0857 AC: 6 AN: 70 Hom.: 0 Cov.: 0 AF XY: 0.109 AC XY: 5 AN XY: 46

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0800

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.132 AC: 20141 AN: 152094 Hom.: 1446 Cov.: 32 AF XY: 0.130 AC XY: 9701 AN XY: 74348

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.0208

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.129

Alfa AF: 0.137 Hom.: 195

Bravo AF: 0.129

Asia WGS AF: 0.0790 AC: 278 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	6.3
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41309831; hg19: chr20-18774864;