20-12982070-A-G

Variant names:

• chr20-12982070-A-G
• rs364585
• ENST00000669657.1:n.874+14860A>G

Variant summary

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

The ENST00000669657.1(LINC01723):​n.874+14860A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 151,946 control chromosomes in the GnomAD database, including 36,767 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 0.69 (36767 hom., cov: 31)
• Consequence: LINC01723 ENST00000669657.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

Genes affected

LINC01723 (HGNC:52511): (long intergenic non-protein coding RNA 1723)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 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
LINC01723	ENST00000669657.1	n.874+14860A>G		intron_variant	Intron 4 of 4
LINC01723	ENST00000670547.1	n.877-12840A>G		intron_variant	Intron 4 of 5
LINC01723	ENST00000671262.1	n.870+14860A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104728 AN: 151828 Hom.: 36723 Cov.: 31

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.690 AC: 104832 AN: 151946 Hom.: 36767 Cov.: 31 AF XY: 0.692 AC XY: 51367 AN XY: 74282

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.574

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.689

Alfa AF: 0.626 Hom.: 34552

Bravo AF: 0.695

Asia WGS AF: 0.659 AC: 2294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs364585; hg19: chr20-12962718;