rs1951039

Positions:

• 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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02306	ENST00000546412.2	n.538-30428A>G		intron_variant, non_coding_transcript_variant		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;