chr14-96747780-A-G

Variant names:

• chr14-96747780-A-G
• rs912343
• ENST00000556669.2:n.155+3511A>G

Variant summary

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

The NR_146552.1(LINC02299):​n.130+3511A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,234 control chromosomes in the GnomAD database, including 2,737 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 0.19 (2737 hom., cov: 33)
• Consequence: LINC02299 NR_146552.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998
• Publications: 8 publications found

Genes affected

LINC02299 (HGNC:53218): (long intergenic non-protein coding RNA 2299)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_146552.1. 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
	LINC02299	NR_146552.1		n.130+3511A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02299	ENST00000556669.2	TSL:5	n.155+3511A>G		intron	N/A
	LINC02299	ENST00000650059.1		n.159+3511A>G		intron	N/A
	LINC02299	ENST00000654843.2		n.141+3511A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28473 AN: 152116 Hom.: 2737 Cov.: 33

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.187 AC: 28481 AN: 152234 Hom.: 2737 Cov.: 33 AF XY: 0.189 AC XY: 14053 AN XY: 74432

African (AFR) AF: 0.218 AC: 9039 AN: 41524

American (AMR) AF: 0.126 AC: 1933 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 715 AN: 3472

East Asian (EAS) AF: 0.128 AC: 661 AN: 5174

South Asian (SAS) AF: 0.254 AC: 1224 AN: 4828

European-Finnish (FIN) AF: 0.199 AC: 2105 AN: 10600

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12257 AN: 68020

Other (OTH) AF: 0.183 AC: 388 AN: 2116

Alfa AF: 0.181 Hom.: 9376

Bravo AF: 0.179

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.47
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs912343; hg19: chr14-97214117;