3-842168-G-A

Position:

• chr3-842168-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.212-208G>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 0.562 in 151,930 control chromosomes in the GnomAD database, including 24,651 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 0.56 (24651 hom., cov: 32)
• Consequence: LINC01266 NR_110118.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01266	NR_110118.1	n.212-208G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01266	ENST00000661103.1	n.382-208G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85253 AN: 151814 Hom.: 24636 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.562 AC: 85322 AN: 151930 Hom.: 24651 Cov.: 32 AF XY: 0.560 AC XY: 41581 AN XY: 74252

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.696

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.563

Alfa AF: 0.619 Hom.: 62376

Bravo AF: 0.553

Asia WGS AF: 0.477 AC: 1661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4684585; hg19: chr3-883851;