chr20-24137946-G-A

Variant names:

• chr20-24137946-G-A
• rs1555286
• ENST00000664459.1:n.375+4297G>A

Variant summary

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

The ENST00000664459.1(LINC01721):​n.375+4297G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 152,086 control chromosomes in the GnomAD database, including 16,088 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 0.46 (16088 hom., cov: 33)
• Consequence: LINC01721 ENST00000664459.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273
• Publications: 5 publications found

Genes affected

LINC01721 (HGNC:52508): (long intergenic non-protein coding RNA 1721)

ENSG00000298235 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664459.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01721	ENST00000664459.1		n.375+4297G>A		intron	N/A
	LINC01721	ENST00000669143.1		n.444+4297G>A		intron	N/A
	LINC01721	ENST00000753590.1		n.184-24023G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69568 AN: 151968 Hom.: 16083 Cov.: 33

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.494

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.458 AC: 69597 AN: 152086 Hom.: 16088 Cov.: 33 AF XY: 0.462 AC XY: 34324 AN XY: 74342

African (AFR) AF: 0.396 AC: 16422 AN: 41466

American (AMR) AF: 0.446 AC: 6818 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1711 AN: 3468

East Asian (EAS) AF: 0.564 AC: 2913 AN: 5164

South Asian (SAS) AF: 0.475 AC: 2290 AN: 4826

European-Finnish (FIN) AF: 0.563 AC: 5952 AN: 10572

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31976 AN: 67978

Other (OTH) AF: 0.490 AC: 1037 AN: 2116

Alfa AF: 0.467 Hom.: 34151

Bravo AF: 0.445

Asia WGS AF: 0.515 AC: 1793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.21
DANN	Benign	0.65
PhyloP100		-0.27

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: rs1555286;

hg19: chr20-24118582;