ENST00000546412.2:n.200-1244T>C

Variant names:

• chr14-26127459-A-G
• rs6574794
• ENST00000546412.2:n.200-1244T>C

Variant summary

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

The ENST00000546412.2(LINC02306):​n.200-1244T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364
• 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=-0.99).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02306	ENST00000546412.2	n.200-1244T>C		intron_variant	Intron 1 of 9	3
LINC02306	ENST00000657312.2	n.656+23T>C		intron_variant	Intron 2 of 6

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

African (AFR) AF: 0.774 AC: 32141 AN: 41500

American (AMR) AF: 0.924 AC: 14124 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.959 AC: 3326 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5172 AN: 5174

South Asian (SAS) AF: 0.966 AC: 4663 AN: 4828

European-Finnish (FIN) AF: 0.955 AC: 10133 AN: 10612

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.954 AC: 64870 AN: 68026

Other (OTH) AF: 0.916 AC: 1934 AN: 2112

Alfa AF: 0.904 Hom.: 38372

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
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs6574794; hg19: chr14-26596665;