ENST00000669643.1:n.1116C>G

Variant names:

• chr21-20684874-G-C
• rs2826473
• ENST00000669643.1:n.1116C>G

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00320	ENST00000669643.1	n.1116C>G		non_coding_transcript_exon_variant	Exon 8 of 8
LINC00320	ENST00000655781.1	n.142-7687C>G		intron_variant	Intron 2 of 3

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;