rs17047538

chr3-758923-A-G

Variant summary

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

The NR_110118.1(LINC01266):n.115+8673A>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 0.287 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 NR_110118.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01266	NR_110118.1	n.115+8673A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01266	ENST00000661103.1	n.381+8673A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.263

Alfa AF: 0.326 Hom.: 5091

Bravo AF: 0.271

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.5
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17047538; hg19: chr3-800606;