rs2415836

chr14-44071357-A-Cchr14-44071357-A-Gchr14-44071357-A-T

Variant summary

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

The ENST00000654351.1(LINC02307):n.172-21850T>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 0.858 in 151,610 control chromosomes in the GnomAD database, including 56,484 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 0.86 (56484 hom., cov: 31)
• Consequence: LINC02307 ENST00000654351.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580

Genes affected

LINC02307 (HGNC:53226): (long intergenic non-protein coding RNA 2307)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.958 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
LINC02307	ENST00000654351.1	n.172-21850T>G		intron_variant, non_coding_transcript_variant
LINC02307	ENST00000553827.1	n.70-21850T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.858 AC: 130009 AN: 151494 Hom.: 56414 Cov.: 31

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.858 AC: 130139 AN: 151610 Hom.: 56484 Cov.: 31 AF XY: 0.851 AC XY: 63058 AN XY: 74076

Gnomad4 AFR AF: 0.966

Gnomad4 AMR AF: 0.802

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.748

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.848

Gnomad4 OTH AF: 0.834

Alfa AF: 0.845 Hom.: 25852

Bravo AF: 0.863

Asia WGS AF: 0.678 AC: 2358 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.89
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2415836; hg19: chr14-44540560;