3-713686-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420823.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01266	NR_110118.1		n.80-36529T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01266	ENST00000420823.5	TSL:2	n.177-36529T>C		intron	N/A
	LINC01266	ENST00000442809.1	TSL:4	n.155-36529T>C		intron	N/A
	LINC01266	ENST00000653731.1		n.216-36172T>C		intron	N/A

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

African (AFR) AF: 0.521 AC: 21564 AN: 41414

American (AMR) AF: 0.334 AC: 5097 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1024 AN: 3470

East Asian (EAS) AF: 0.393 AC: 2027 AN: 5160

South Asian (SAS) AF: 0.350 AC: 1684 AN: 4806

European-Finnish (FIN) AF: 0.404 AC: 4254 AN: 10542

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17770 AN: 67926

Other (OTH) AF: 0.322 AC: 680 AN: 2112

Alfa AF: 0.278 Hom.: 4542

Bravo AF: 0.359

Asia WGS AF: 0.391 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.37
PhyloP100		-0.76

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12715600;

hg19: chr3-755370;