20-21627926-T-C

Position:

• chr20-21627926-T-C

Variant summary

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

The NR_109878.1(LINC01726):​n.265-484A>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 0.649 in 152,082 control chromosomes in the GnomAD database, including 34,042 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 0.65 (34042 hom., cov: 32)
• Consequence: LINC01726 NR_109878.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01726	NR_109878.1	n.265-484A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01726	ENST00000624692.1	n.265-484A>G		intron_variant, non_coding_transcript_variant		1
LINC01727	ENST00000655574.1	n.746+12038T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98664 AN: 151964 Hom.: 34046 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.649 AC: 98679 AN: 152082 Hom.: 34042 Cov.: 32 AF XY: 0.650 AC XY: 48302 AN XY: 74360

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.680

Alfa AF: 0.708 Hom.: 4944

Bravo AF: 0.624

Asia WGS AF: 0.575 AC: 2002 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs970177; hg19: chr20-21608564;