rs680379

chr20-12988752-A-Gchr20-12988752-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01723	ENST00000669657.1	n.875-19306A>G		intron_variant, non_coding_transcript_variant
LINC01723	ENST00000670547.1	n.877-6158A>G		intron_variant, non_coding_transcript_variant
LINC01723	ENST00000671262.1	n.871-19306A>G		intron_variant, non_coding_transcript_variant

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;