chr14-26019261-T-C

Variant names:

• chr14-26019261-T-C
• rs862946
• ENST00000546412.2:n.258+106896A>G

Variant summary

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

The ENST00000546412.2(LINC02306):​n.258+106896A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 152,040 control chromosomes in the GnomAD database, including 45,077 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 0.77 (45077 hom., cov: 31)
• Consequence: LINC02306 ENST00000546412.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.832 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.258+106896A>G		intron_variant	Intron 2 of 9	3
LINC02306	ENST00000657312.2	n.715+106896A>G		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116880 AN: 151922 Hom.: 45035 Cov.: 31

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.769 AC: 116978 AN: 152040 Hom.: 45077 Cov.: 31 AF XY: 0.770 AC XY: 57266 AN XY: 74328

African (AFR) AF: 0.774 AC: 32105 AN: 41474

American (AMR) AF: 0.805 AC: 12301 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2496 AN: 3472

East Asian (EAS) AF: 0.828 AC: 4241 AN: 5124

South Asian (SAS) AF: 0.854 AC: 4111 AN: 4816

European-Finnish (FIN) AF: 0.729 AC: 7726 AN: 10592

Middle Eastern (MID) AF: 0.760 AC: 222 AN: 292

European-Non Finnish (NFE) AF: 0.755 AC: 51333 AN: 67964

Other (OTH) AF: 0.763 AC: 1614 AN: 2114

Alfa AF: 0.762 Hom.: 79052

Bravo AF: 0.773

Asia WGS AF: 0.850 AC: 2958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.47
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs862946; hg19: chr14-26488467;