rs970177

Variant names:

• chr20-21627926-T-C
• rs970177
• ENST00000624692.1:n.265-484A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000624692.1(LINC01726):​n.265-484A>G variant causes a intron 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 ENST00000624692.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 3 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000624692.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01726	NR_109878.1		n.265-484A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01726	ENST00000624692.1	TSL:1	n.265-484A>G		intron	N/A
	LINC01727	ENST00000624367.4	TSL:5	n.801+12038T>C		intron	N/A
	LINC01727	ENST00000653224.1		n.659+12038T>C		intron	N/A

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

African (AFR) AF: 0.412 AC: 17077 AN: 41476

American (AMR) AF: 0.618 AC: 9452 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2794 AN: 3468

East Asian (EAS) AF: 0.613 AC: 3171 AN: 5176

South Asian (SAS) AF: 0.659 AC: 3172 AN: 4810

European-Finnish (FIN) AF: 0.795 AC: 8408 AN: 10578

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52306 AN: 67962

Other (OTH) AF: 0.680 AC: 1439 AN: 2116

Alfa AF: 0.696 Hom.: 5009

Bravo AF: 0.624

Asia WGS AF: 0.575 AC: 2002 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.72
PhyloP100		0.12

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs970177;

hg19: chr20-21608564;