3-713686-T-C

Variant names:

• chr3-713686-T-C
• rs12715600
• ENST00000420823.5:n.177-36529T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000420823.5(LINC01266):​n.177-36529T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,892 control chromosomes in the GnomAD database, including 10,780 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 0.36 (10780 hom., cov: 32)
• Consequence: LINC01266 ENST00000420823.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01266	NR_110118.1	n.80-36529T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01266	ENST00000420823.5	n.177-36529T>C		intron_variant	Intron 2 of 4	2
LINC01266	ENST00000442809.1	n.155-36529T>C		intron_variant	Intron 2 of 4	4
LINC01266	ENST00000653731.1	n.216-36172T>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54319 AN: 151774 Hom.: 10746 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.358 AC: 54406 AN: 151892 Hom.: 10780 Cov.: 32 AF XY: 0.363 AC XY: 26957 AN XY: 74230

Gnomad4 AFR AF: 0.521

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.322

Alfa AF: 0.263 Hom.: 2816

Bravo AF: 0.359

Asia WGS AF: 0.391 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
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: rs12715600; hg19: chr3-755370;