rs680379

Variant names:

• chr20-12988752-A-G
• rs680379
• ENST00000669657.1:n.875-19306A>G

Your query was ambiguous. Multiple possible variants found:

• chr20-12988752-A-G
• chr20-12988752-A-T

Variant summary

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

The ENST00000669657.1(LINC01723):​n.875-19306A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 152,080 control chromosomes in the GnomAD database, including 37,382 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 (37382 hom., cov: 32)
• Consequence: LINC01723 ENST00000669657.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 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.875-19306A>G		intron_variant	Intron 4 of 4
LINC01723	ENST00000670547.1	n.877-6158A>G		intron_variant	Intron 4 of 5
LINC01723	ENST00000671262.1	n.871-19306A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105549 AN: 151962 Hom.: 37334 Cov.: 32

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.695 AC: 105659 AN: 152080 Hom.: 37382 Cov.: 32 AF XY: 0.697 AC XY: 51810 AN XY: 74336

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.689

Alfa AF: 0.630 Hom.: 67793

Bravo AF: 0.699

Asia WGS AF: 0.692 AC: 2408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.16
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs680379; hg19: chr20-12969400;