rs2627923

Positions:

• chr3-607475-G-A

Variant summary

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

The NR_110118.1(LINC01266):​n.79+15292G>A 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 0.158 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 NR_110118.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

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=-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/exons	MANE	Protein	UniProt
LINC01266	NR_110118.1	n.79+15292G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01266	ENST00000661103.1	n.345+15292G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.0991

Gnomad4 ASJ AF: 0.0328

Gnomad4 EAS AF: 0.00370

Gnomad4 SAS AF: 0.0357

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0725

Gnomad4 OTH AF: 0.136

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2627923; hg19: chr3-649158;