3-768037-G-T

Variant names:

• chr3-768037-G-T
• rs11714239
• ENST00000420823.5:n.212+17787G>T

Variant summary

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

The ENST00000420823.5(LINC01266):​n.212+17787G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 151,964 control chromosomes in the GnomAD database, including 15,021 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 0.44 (15021 hom., cov: 33)
• Consequence: LINC01266 ENST00000420823.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.667
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01266	NR_110118.1	n.115+17787G>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01266	ENST00000420823.5	n.212+17787G>T		intron_variant	Intron 3 of 4	2
LINC01266	ENST00000442809.1	n.190+17787G>T		intron_variant	Intron 3 of 4	4
LINC01266	ENST00000653731.1	n.336+17787G>T		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66447 AN: 151846 Hom.: 14996 Cov.: 33

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.438 AC: 66518 AN: 151964 Hom.: 15021 Cov.: 33 AF XY: 0.440 AC XY: 32682 AN XY: 74252

African (AFR) AF: 0.540 AC: 22395 AN: 41454

American (AMR) AF: 0.389 AC: 5943 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1162 AN: 3468

East Asian (EAS) AF: 0.382 AC: 1973 AN: 5170

South Asian (SAS) AF: 0.442 AC: 2131 AN: 4816

European-Finnish (FIN) AF: 0.491 AC: 5171 AN: 10536

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26419 AN: 67948

Other (OTH) AF: 0.388 AC: 817 AN: 2108

Alfa AF: 0.403 Hom.: 21232

Bravo AF: 0.437

Asia WGS AF: 0.416 AC: 1446 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.58
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs11714239; hg19: chr3-809720;