chr20-24267708-C-T

Variant names:

• chr20-24267708-C-T
• rs224786
• ENST00000753590.1:n.429-30601C>T

Variant summary

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

The ENST00000753590.1(LINC01721):​n.429-30601C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 152,084 control chromosomes in the GnomAD database, including 33,196 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 (33196 hom., cov: 33)
• Consequence: LINC01721 ENST00000753590.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 2 publications found

Genes affected

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

ENSG00000232200 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01721	ENST00000753590.1	n.429-30601C>T		intron_variant	Intron 4 of 4
LINC01721	ENST00000753591.1	n.936-30601C>T		intron_variant	Intron 3 of 3
ENSG00000232200	ENST00000753785.1	n.583-2099G>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99079 AN: 151966 Hom.: 33159 Cov.: 33

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.652 AC: 99176 AN: 152084 Hom.: 33196 Cov.: 33 AF XY: 0.653 AC XY: 48507 AN XY: 74332

African (AFR) AF: 0.800 AC: 33200 AN: 41504

American (AMR) AF: 0.530 AC: 8093 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2237 AN: 3466

East Asian (EAS) AF: 0.503 AC: 2598 AN: 5162

South Asian (SAS) AF: 0.546 AC: 2633 AN: 4818

European-Finnish (FIN) AF: 0.717 AC: 7570 AN: 10564

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.603 AC: 40987 AN: 67972

Other (OTH) AF: 0.626 AC: 1324 AN: 2114

Alfa AF: 0.599 Hom.: 34987

Bravo AF: 0.641

Asia WGS AF: 0.518 AC: 1804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.32
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs224786; hg19: chr20-24248344;