21-20790515-C-A

Variant names:

• chr21-20790515-C-A
• rs2826520
• ENST00000435279.7:n.223-4427G>T

Variant summary

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

The ENST00000435279.7(LINC00320):​n.223-4427G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 151,914 control chromosomes in the GnomAD database, including 5,220 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 0.24 (5220 hom., cov: 32)
• Consequence: LINC00320 ENST00000435279.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.946
• Publications: 2 publications found

Genes affected

LINC00320 (HGNC:19690): (long intergenic non-protein coding RNA 320)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435279.7. 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
	LINC00320	NR_024090.2		n.115-4427G>T		intron	N/A
	LINC00320	NR_109786.1		n.115-8069G>T		intron	N/A
	LINC00320	NR_109787.1		n.115-4427G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00320	ENST00000435279.7	TSL:1	n.223-4427G>T		intron	N/A
	LINC00320	ENST00000437238.7	TSL:1	n.303-4427G>T		intron	N/A
	LINC00320	ENST00000452561.6	TSL:1	n.117-8069G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35800 AN: 151796 Hom.: 5222 Cov.: 32

Gnomad AFR AF: 0.0640

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.236 AC: 35805 AN: 151914 Hom.: 5220 Cov.: 32 AF XY: 0.237 AC XY: 17591 AN XY: 74248

African (AFR) AF: 0.0639 AC: 2651 AN: 41460

American (AMR) AF: 0.254 AC: 3875 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1481 AN: 3466

East Asian (EAS) AF: 0.164 AC: 850 AN: 5172

South Asian (SAS) AF: 0.225 AC: 1081 AN: 4810

European-Finnish (FIN) AF: 0.310 AC: 3269 AN: 10552

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21705 AN: 67910

Other (OTH) AF: 0.268 AC: 565 AN: 2108

Alfa AF: 0.293 Hom.: 9914

Bravo AF: 0.224

Asia WGS AF: 0.195 AC: 677 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	1.0
DANN	Benign	0.76
PhyloP100		-0.95

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: rs2826520;

hg19: chr21-22162833;