rs2826520

chr21-20790515-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_109786.1(LINC00320):n.115-8069G>T variant causes a intron, non coding transcript 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 NR_109786.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.946

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00320	NR_109786.1	n.115-8069G>T		intron_variant, non_coding_transcript_variant
LINC00320	NR_024090.2	n.115-4427G>T		intron_variant, non_coding_transcript_variant
LINC00320	NR_109787.1	n.115-4427G>T		intron_variant, non_coding_transcript_variant
LINC00320	NR_109788.1	n.115-4427G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00320	ENST00000669643.1	n.61-8069G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0639

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.268

Alfa AF: 0.307 Hom.: 7121

Bravo AF: 0.224

Asia WGS AF: 0.195 AC: 677 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	1.0
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2826520; hg19: chr21-22162833;