20-24259293-G-C

Variant names:

• chr20-24259293-G-C
• rs224788
• ENST00000753590.1:n.429-39016G>C

Variant summary

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

The ENST00000753590.1(LINC01721):​n.429-39016G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 152,134 control chromosomes in the GnomAD database, including 33,499 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 0.65 (33499 hom., cov: 33)
• Consequence: LINC01721 ENST00000753590.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.44
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000753590.1. 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	ENST00000753590.1		n.429-39016G>C		intron	N/A
	LINC01721	ENST00000753591.1		n.936-39016G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99552 AN: 152016 Hom.: 33462 Cov.: 33

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.655 AC: 99647 AN: 152134 Hom.: 33499 Cov.: 33 AF XY: 0.656 AC XY: 48781 AN XY: 74376

African (AFR) AF: 0.800 AC: 33238 AN: 41530

American (AMR) AF: 0.530 AC: 8105 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2259 AN: 3470

East Asian (EAS) AF: 0.505 AC: 2602 AN: 5156

South Asian (SAS) AF: 0.548 AC: 2640 AN: 4816

European-Finnish (FIN) AF: 0.728 AC: 7712 AN: 10588

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41226 AN: 67974

Other (OTH) AF: 0.627 AC: 1324 AN: 2110

Alfa AF: 0.634 Hom.: 3900

Bravo AF: 0.643

Asia WGS AF: 0.523 AC: 1822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.055
DANN	Benign	0.76
PhyloP100		-4.4

Splicing

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

Other links and lift over

dbSNP: rs224788; hg19: chr20-24239929;