chr21-20224897-G-A

Variant names:

• chr21-20224897-G-A
• rs2826103
• ENST00000746617.1:n.81-19466C>T

Variant summary

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

The ENST00000746617.1(LINC02573):​n.81-19466C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0809 in 151,886 control chromosomes in the GnomAD database, including 739 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 0.081 (739 hom., cov: 32)
• Consequence: LINC02573 ENST00000746617.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 1 publications found

Genes affected

LINC02573 (HGNC:53730): (long intergenic non-protein coding RNA 2573)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.194 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
LINC02573	ENST00000746617.1	n.81-19466C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0807 AC: 12253 AN: 151774 Hom.: 735 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.0454

Gnomad FIN AF: 0.0383

Gnomad MID AF: 0.0428

Gnomad NFE AF: 0.0450

Gnomad OTH AF: 0.0830

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

GnomAD4 genome AF: 0.0809 AC: 12281 AN: 151886 Hom.: 739 Cov.: 32 AF XY: 0.0835 AC XY: 6194 AN XY: 74222

African (AFR) AF: 0.101 AC: 4177 AN: 41492

American (AMR) AF: 0.200 AC: 3045 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.0720 AC: 250 AN: 3470

East Asian (EAS) AF: 0.170 AC: 875 AN: 5148

South Asian (SAS) AF: 0.0450 AC: 217 AN: 4822

European-Finnish (FIN) AF: 0.0383 AC: 403 AN: 10528

Middle Eastern (MID) AF: 0.0461 AC: 13 AN: 282

European-Non Finnish (NFE) AF: 0.0450 AC: 3054 AN: 67890

Other (OTH) AF: 0.0831 AC: 175 AN: 2106

Alfa AF: 0.0607 Hom.: 64

Bravo AF: 0.0967

Asia WGS AF: 0.0910 AC: 315 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.28
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2826103; hg19: chr21-21597210;