rs2627923

Variant names:

• chr3-607475-G-A
• rs2627923
• ENST00000420823.5:n.176+15292G>A

Variant summary

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

The ENST00000420823.5(LINC01266):​n.176+15292G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 150,092 control chromosomes in the GnomAD database, including 3,392 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 0.16 (3392 hom., cov: 31)
• Consequence: LINC01266 ENST00000420823.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 0 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01266	NR_110118.1	n.79+15292G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01266	ENST00000420823.5	n.176+15292G>A		intron_variant	Intron 2 of 4	2
LINC01266	ENST00000442809.1	n.154+15292G>A		intron_variant	Intron 2 of 4	4
LINC01266	ENST00000653731.1	n.215+54621G>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23662 AN: 149972 Hom.: 3370 Cov.: 31

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0993

Gnomad ASJ AF: 0.0328

Gnomad EAS AF: 0.00369

Gnomad SAS AF: 0.0349

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.116

Gnomad NFE AF: 0.0725

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.158 AC: 23733 AN: 150092 Hom.: 3392 Cov.: 31 AF XY: 0.156 AC XY: 11447 AN XY: 73294

African (AFR) AF: 0.387 AC: 15653 AN: 40414

American (AMR) AF: 0.0991 AC: 1492 AN: 15050

Ashkenazi Jewish (ASJ) AF: 0.0328 AC: 113 AN: 3450

East Asian (EAS) AF: 0.00370 AC: 19 AN: 5138

South Asian (SAS) AF: 0.0357 AC: 172 AN: 4814

European-Finnish (FIN) AF: 0.101 AC: 1058 AN: 10484

Middle Eastern (MID) AF: 0.125 AC: 36 AN: 288

European-Non Finnish (NFE) AF: 0.0725 AC: 4888 AN: 67452

Other (OTH) AF: 0.136 AC: 285 AN: 2090

Alfa AF: 0.241 Hom.: 260

Bravo AF: 0.171

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.90
DANN	Benign	0.44
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs2627923; hg19: chr3-649158;