rs6047533

chr20-21641440-G-A

Variant summary

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

The NR_109878.1(LINC01726):n.265-13998C>T 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 0.0701 in 152,264 control chromosomes in the GnomAD database, including 702 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 0.070 (702 hom., cov: 32)
• Consequence: LINC01726 NR_109878.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.816

Genes affected

LINC01726 (HGNC:52514): (long intergenic non-protein coding RNA 1726)

LINC01727 (HGNC:52515): (long intergenic non-protein coding RNA 1727)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01726	NR_109878.1	n.265-13998C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01726	ENST00000624692.1	n.265-13998C>T		intron_variant, non_coding_transcript_variant		1
LINC01727	ENST00000655574.1	n.747-24638G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0698 AC: 10622 AN: 152146 Hom.: 695 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0668

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0478

Gnomad FIN AF: 0.00414

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0190

Gnomad OTH AF: 0.0536

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

GnomAD4 genome AF: 0.0701 AC: 10669 AN: 152264 Hom.: 702 Cov.: 32 AF XY: 0.0683 AC XY: 5085 AN XY: 74462

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.0673

Gnomad4 ASJ AF: 0.0467

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.0478

Gnomad4 FIN AF: 0.00414

Gnomad4 NFE AF: 0.0190

Gnomad4 OTH AF: 0.0531

Alfa AF: 0.0300 Hom.: 257

Bravo AF: 0.0823

Asia WGS AF: 0.101 AC: 352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	6.1
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6047533; hg19: chr20-21622078;