rs2826473

Positions:

• chr21-20684874-G-C

Variant summary

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

The ENST00000669643.1(LINC00320):​n.1116C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0629 in 152,150 control chromosomes in the GnomAD database, including 337 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 0.063 (337 hom., cov: 32)
• Consequence: LINC00320 ENST00000669643.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15

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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00320	ENST00000669643.1	n.1116C>G		non_coding_transcript_exon_variant	8/8
LINC00320	ENST00000655781.1	n.142-7687C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0629 AC: 9557 AN: 152032 Hom.: 335 Cov.: 32

Gnomad AFR AF: 0.0565

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.0680

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0457

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0482

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0582

Gnomad OTH AF: 0.0801

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

GnomAD4 genome AF: 0.0629 AC: 9570 AN: 152150 Hom.: 337 Cov.: 32 AF XY: 0.0635 AC XY: 4722 AN XY: 74394

Gnomad4 AFR AF: 0.0567

Gnomad4 AMR AF: 0.0681

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.0458

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.0482

Gnomad4 NFE AF: 0.0582

Gnomad4 OTH AF: 0.0792

Alfa AF: 0.0652 Hom.: 49

Bravo AF: 0.0646

Asia WGS AF: 0.0980 AC: 339 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2826473; hg19: chr21-22057188;