11-134778949-A-G

Variant names:

• chr11-134778949-A-G
• rs1289444
• ENST00000701514.2:n.353+16225A>G

Variant summary

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

The ENST00000701514.2(LINC02714):​n.353+16225A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 152,042 control chromosomes in the GnomAD database, including 11,839 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 0.39 (11839 hom., cov: 33)
• Consequence: LINC02714 ENST00000701514.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.773
• Publications: 2 publications found

Genes affected

LINC02714 (HGNC:54231): (long intergenic non-protein coding RNA 2714)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000701514.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02714	ENST00000701514.2		n.353+16225A>G		intron	N/A
	LINC02714	ENST00000736257.1		n.177+16225A>G		intron	N/A
	LINC02714	ENST00000736258.1		n.177+16225A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59549 AN: 151924 Hom.: 11836 Cov.: 33

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.392 AC: 59588 AN: 152042 Hom.: 11839 Cov.: 33 AF XY: 0.395 AC XY: 29351 AN XY: 74296

African (AFR) AF: 0.325 AC: 13486 AN: 41492

American (AMR) AF: 0.475 AC: 7265 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1276 AN: 3458

East Asian (EAS) AF: 0.462 AC: 2385 AN: 5164

South Asian (SAS) AF: 0.390 AC: 1879 AN: 4822

European-Finnish (FIN) AF: 0.407 AC: 4289 AN: 10540

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27617 AN: 67970

Other (OTH) AF: 0.421 AC: 891 AN: 2114

Alfa AF: 0.396 Hom.: 7605

Bravo AF: 0.401

Asia WGS AF: 0.417 AC: 1451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.3
DANN	Benign	0.56
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs1289444; hg19: chr11-134648843;