rs1586218

chr3-694543-A-Gchr3-694543-A-T

Variant summary

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

The NR_110118.1(LINC01266):n.80-55672A>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 0.631 in 151,988 control chromosomes in the GnomAD database, including 32,203 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 0.63 (32203 hom., cov: 32)
• Consequence: LINC01266 NR_110118.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01266	NR_110118.1	n.80-55672A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01266	ENST00000661103.1	n.346-55672A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.632 AC: 95933 AN: 151870 Hom.: 32206 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.631 AC: 95954 AN: 151988 Hom.: 32203 Cov.: 32 AF XY: 0.629 AC XY: 46733 AN XY: 74276

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.756

Gnomad4 OTH AF: 0.665

Alfa AF: 0.671 Hom.: 5142

Bravo AF: 0.623

Asia WGS AF: 0.613 AC: 2131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.5
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1586218; hg19: chr3-736227;