chr3-694543-A-G

Variant names:

• chr3-694543-A-G
• rs1586218
• ENST00000420823.5:n.177-55672A>G

Variant summary

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

The ENST00000420823.5(LINC01266):​n.177-55672A>G variant causes a intron 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 ENST00000420823.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 0 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=-0.92).
• 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 rank	MANE	Protein	UniProt
LINC01266	NR_110118.1	n.80-55672A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01266	ENST00000420823.5	n.177-55672A>G		intron_variant	Intron 2 of 4	2
LINC01266	ENST00000442809.1	n.155-55672A>G		intron_variant	Intron 2 of 4	4
LINC01266	ENST00000653731.1	n.216-55315A>G		intron_variant	Intron 2 of 5

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

African (AFR) AF: 0.397 AC: 16454 AN: 41432

American (AMR) AF: 0.667 AC: 10175 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2440 AN: 3464

East Asian (EAS) AF: 0.625 AC: 3231 AN: 5168

South Asian (SAS) AF: 0.658 AC: 3172 AN: 4818

European-Finnish (FIN) AF: 0.645 AC: 6811 AN: 10558

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51376 AN: 67974

Other (OTH) AF: 0.665 AC: 1401 AN: 2108

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
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1586218; hg19: chr3-736227;