chr14-25737460-T-A

Position:

• chr14-25737460-T-A

Variant summary

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

The ENST00000546412.2(LINC02306):​n.538-72485A>T 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 0.707 in 151,980 control chromosomes in the GnomAD database, including 38,312 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 0.71 (38312 hom., cov: 32)
• Consequence: LINC02306 ENST00000546412.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02306	ENST00000546412.2	n.538-72485A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107318 AN: 151862 Hom.: 38299 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.707 AC: 107380 AN: 151980 Hom.: 38312 Cov.: 32 AF XY: 0.713 AC XY: 52966 AN XY: 74298

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.727

Gnomad4 OTH AF: 0.738

Alfa AF: 0.704 Hom.: 4708

Bravo AF: 0.700

Asia WGS AF: 0.812 AC: 2825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.3
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2877739; hg19: chr14-26206666;