14-96747780-A-G

Position:

• chr14-96747780-A-G

Variant summary

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

The NR_146552.1(LINC02299):​n.130+3511A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02299	NR_146552.1	n.130+3511A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02299	ENST00000650059.1	n.159+3511A>G		intron_variant, non_coding_transcript_variant
LINC02299	ENST00000556669.1	n.130+3511A>G		intron_variant, non_coding_transcript_variant		5
LINC02299	ENST00000654843.1	n.140+3511A>G		intron_variant, non_coding_transcript_variant
LINC02299	ENST00000664687.1	n.131+3511A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.183

Alfa AF: 0.181 Hom.: 3892

Bravo AF: 0.179

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs912343; hg19: chr14-97214117;