rs1951039

Variant names:

• chr14-25695403-T-C
• rs1951039
• ENST00000546412.2:n.538-30428A>G

Your query was ambiguous. Multiple possible variants found:

• chr14-25695403-T-C
• chr14-25695403-T-G

Variant summary

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

The ENST00000546412.2(LINC02306):​n.538-30428A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 151,852 control chromosomes in the GnomAD database, including 15,084 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 0.42 (15084 hom., cov: 31)
• Consequence: LINC02306 ENST00000546412.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.512 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.538-30428A>G		intron_variant	Intron 5 of 9	3

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63912 AN: 151734 Hom.: 15088 Cov.: 31

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.421 AC: 63905 AN: 151852 Hom.: 15084 Cov.: 31 AF XY: 0.422 AC XY: 31288 AN XY: 74206

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.472

Alfa AF: 0.507 Hom.: 41829

Bravo AF: 0.415

Asia WGS AF: 0.296 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1951039; hg19: chr14-26164609;