rs4684585

Variant names:

• chr3-842168-G-A
• rs4684585
• ENST00000420823.5:n.309-208G>A

Variant summary

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

The ENST00000420823.5(LINC01266):​n.309-208G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,930 control chromosomes in the GnomAD database, including 24,651 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 0.56 (24651 hom., cov: 32)
• Consequence: LINC01266 ENST00000420823.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 6 publications found

Genes affected

LINC01266 (HGNC:50309): (long intergenic non-protein coding RNA 1266)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420823.5. 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
	LINC01266	NR_110118.1		n.212-208G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01266	ENST00000420823.5	TSL:2	n.309-208G>A		intron	N/A
	LINC01266	ENST00000442809.1	TSL:4	n.318-208G>A		intron	N/A
	LINC01266	ENST00000653731.1		n.433-208G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85253 AN: 151814 Hom.: 24636 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.562 AC: 85322 AN: 151930 Hom.: 24651 Cov.: 32 AF XY: 0.560 AC XY: 41581 AN XY: 74252

African (AFR) AF: 0.430 AC: 17811 AN: 41416

American (AMR) AF: 0.539 AC: 8235 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2412 AN: 3464

East Asian (EAS) AF: 0.445 AC: 2290 AN: 5150

South Asian (SAS) AF: 0.535 AC: 2577 AN: 4818

European-Finnish (FIN) AF: 0.640 AC: 6749 AN: 10548

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.637 AC: 43267 AN: 67948

Other (OTH) AF: 0.563 AC: 1190 AN: 2114

Alfa AF: 0.606 Hom.: 87322

Bravo AF: 0.553

Asia WGS AF: 0.477 AC: 1661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.37
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs4684585; hg19: chr3-883851;