20-18794220-C-T

Variant names:

• chr20-18794220-C-T
• rs41309831
• ENST00000454749.1:n.70G>A

Variant summary

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

The ENST00000454749.1(LINC00652):​n.70G>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 ENST00000454749.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 2 publications found

Genes affected

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

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000454749.1. 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
	LINC00652	NR_026883.1		n.365G>A		non_coding_transcript_exon	Exon 1 of 4
	LCDR	NR_026885.1		n.172C>T		non_coding_transcript_exon	Exon 1 of 1
	LINC00652	NR_026884.1		n.-238G>A		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00652	ENST00000454749.1	TSL:1	n.70G>A		non_coding_transcript_exon	Exon 1 of 5
	LINC00652	ENST00000455340.6	TSL:2	n.103G>A		non_coding_transcript_exon	Exon 1 of 5
	LCDR	ENST00000609087.2	TSL:6	n.143C>T		non_coding_transcript_exon	Exon 1 of 1

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

African (AFR) AF: 0.00 AC: 0 AN: 6

American (AMR) AC: 0 AN: 0

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0800 AC: 4 AN: 50

Other (OTH) AF: 0.250 AC: 1 AN: 4

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

African (AFR) AF: 0.103 AC: 4292 AN: 41510

American (AMR) AF: 0.118 AC: 1810 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 380 AN: 3466

East Asian (EAS) AF: 0.0208 AC: 107 AN: 5152

South Asian (SAS) AF: 0.117 AC: 563 AN: 4826

European-Finnish (FIN) AF: 0.159 AC: 1681 AN: 10584

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10870 AN: 67954

Other (OTH) AF: 0.129 AC: 272 AN: 2114

Alfa AF: 0.139 Hom.: 414

Bravo AF: 0.129

Asia WGS AF: 0.0790 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.3
DANN	Benign	0.65
PhyloP100		0.20

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs41309831;

hg19: chr20-18774864;