3-636663-A-G

Position:

• chr3-636663-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.79+44480A>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 0.479 in 151,838 control chromosomes in the GnomAD database, including 18,150 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 0.48 (18150 hom., cov: 31)
• Consequence: LINC01266 NR_110118.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01266	NR_110118.1	n.79+44480A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01266	ENST00000661103.1	n.345+44480A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72698 AN: 151720 Hom.: 18142 Cov.: 31

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.479 AC: 72736 AN: 151838 Hom.: 18150 Cov.: 31 AF XY: 0.484 AC XY: 35893 AN XY: 74180

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.478

Alfa AF: 0.508 Hom.: 27693

Bravo AF: 0.482

Asia WGS AF: 0.538 AC: 1872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.2
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1351865; hg19: chr3-678347;