14-26127459-A-G

Position:

• chr14-26127459-A-G

Variant summary

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

The ENST00000546412.2(LINC02306):​n.200-1244T>C 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 0.903 in 152,216 control chromosomes in the GnomAD database, including 62,651 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 0.90 (62651 hom., cov: 32)
• Consequence: LINC02306 ENST00000546412.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364

Genes affected

LINC02306 (HGNC:53225): (long intergenic non-protein coding RNA 2306)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02306	ENST00000546412.2	n.200-1244T>C		intron_variant, non_coding_transcript_variant		3
LINC02306	ENST00000657312.1	n.399+23T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.903 AC: 137416 AN: 152098 Hom.: 62601 Cov.: 32

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.924

Gnomad ASJ AF: 0.959

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.954

Gnomad OTH AF: 0.915

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

GnomAD4 genome AF: 0.903 AC: 137523 AN: 152216 Hom.: 62651 Cov.: 32 AF XY: 0.906 AC XY: 67399 AN XY: 74410

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.924

Gnomad4 ASJ AF: 0.959

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.966

Gnomad4 FIN AF: 0.955

Gnomad4 NFE AF: 0.954

Gnomad4 OTH AF: 0.916

Alfa AF: 0.933 Hom.: 13095

Bravo AF: 0.895

Asia WGS AF: 0.966 AC: 3360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6574794; hg19: chr14-26596665;