rs2877739

Variant names:

• chr14-25737460-T-A
• rs2877739
• ENST00000546412.2:n.538-72485A>T

Your query was ambiguous. Multiple possible variants found:

• chr14-25737460-T-A
• chr14-25737460-T-C
• chr14-25737460-T-G

Variant summary

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

The ENST00000546412.2(LINC02306):​n.538-72485A>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000546412.2. 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
	LINC02306	ENST00000546412.2	TSL:3	n.538-72485A>T		intron	N/A
	LINC02306	ENST00000736904.1		n.280-72485A>T		intron	N/A

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

African (AFR) AF: 0.592 AC: 24505 AN: 41418

American (AMR) AF: 0.761 AC: 11601 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2875 AN: 3470

East Asian (EAS) AF: 0.836 AC: 4312 AN: 5160

South Asian (SAS) AF: 0.824 AC: 3965 AN: 4814

European-Finnish (FIN) AF: 0.771 AC: 8149 AN: 10576

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.727 AC: 49432 AN: 67970

Other (OTH) AF: 0.738 AC: 1560 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.3
DANN	Benign	0.83
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs2877739; hg19: chr14-26206666;