3-758923-A-G

Variant names:

• chr3-758923-A-G
• rs17047538
• ENST00000420823.5:n.212+8673A>G

Variant summary

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

The ENST00000420823.5(LINC01266):​n.212+8673A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,052 control chromosomes in the GnomAD database, including 6,898 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 0.29 (6898 hom., cov: 32)
• Consequence: LINC01266 ENST00000420823.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.39 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01266	NR_110118.1		n.115+8673A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01266	ENST00000420823.5	TSL:2	n.212+8673A>G		intron	N/A
	LINC01266	ENST00000442809.1	TSL:4	n.190+8673A>G		intron	N/A
	LINC01266	ENST00000653731.1		n.336+8673A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43606 AN: 151936 Hom.: 6892 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.287 AC: 43634 AN: 152052 Hom.: 6898 Cov.: 32 AF XY: 0.293 AC XY: 21793 AN XY: 74328

African (AFR) AF: 0.156 AC: 6468 AN: 41538

American (AMR) AF: 0.281 AC: 4296 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 835 AN: 3468

East Asian (EAS) AF: 0.341 AC: 1756 AN: 5154

South Asian (SAS) AF: 0.405 AC: 1949 AN: 4810

European-Finnish (FIN) AF: 0.413 AC: 4361 AN: 10552

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.339 AC: 23018 AN: 67940

Other (OTH) AF: 0.263 AC: 555 AN: 2110

Alfa AF: 0.327 Hom.: 5546

Bravo AF: 0.271

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.68
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs17047538; hg19: chr3-800606;