3-636663-A-G

Variant names:

• chr3-636663-A-G
• rs1351865
• ENST00000420823.5:n.176+44480A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000420823.5(LINC01266):​n.176+44480A>G variant causes a intron 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 ENST00000420823.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01266	NR_110118.1	n.79+44480A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01266	ENST00000420823.5	n.176+44480A>G		intron_variant	Intron 2 of 4	2
LINC01266	ENST00000442809.1	n.154+44480A>G		intron_variant	Intron 2 of 4	4
LINC01266	ENST00000653731.1	n.215+83809A>G		intron_variant	Intron 2 of 5

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

African (AFR) AF: 0.342 AC: 14178 AN: 41434

American (AMR) AF: 0.598 AC: 9098 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1876 AN: 3468

East Asian (EAS) AF: 0.674 AC: 3481 AN: 5164

South Asian (SAS) AF: 0.567 AC: 2729 AN: 4814

European-Finnish (FIN) AF: 0.491 AC: 5175 AN: 10532

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34509 AN: 67906

Other (OTH) AF: 0.478 AC: 1009 AN: 2112

Alfa AF: 0.505 Hom.: 37847

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
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs1351865; hg19: chr3-678347;