rs862946

chr14-26019261-T-C

Variant summary

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

The ENST00000546412.2(LINC02306):n.258+106896A>G 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 0.769 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251

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=-0.88).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02306	ENST00000546412.2	n.258+106896A>G		intron_variant, non_coding_transcript_variant		3
LINC02306	ENST00000657312.1	n.458+106896A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.828

Gnomad4 SAS AF: 0.854

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.755

Gnomad4 OTH AF: 0.763

Alfa AF: 0.760 Hom.: 57775

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs862946; hg19: chr14-26488467;