rs2415836

Variant names:

• chr14-44071357-A-C
• rs2415836
• ENST00000553827.1:n.70-21850T>G

Your query was ambiguous. Multiple possible variants found:

• chr14-44071357-A-C
• chr14-44071357-A-G
• chr14-44071357-A-T

Variant summary

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

The ENST00000553827.1(LINC02307):​n.70-21850T>G variant causes a intron 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 ENST00000553827.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553827.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02307	NR_187192.1		n.169-21850T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02307	ENST00000553827.1	TSL:3	n.70-21850T>G		intron	N/A
	LINC02307	ENST00000654351.1		n.172-21850T>G		intron	N/A

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

African (AFR) AF: 0.966 AC: 40063 AN: 41460

American (AMR) AF: 0.802 AC: 12146 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2886 AN: 3464

East Asian (EAS) AF: 0.540 AC: 2760 AN: 5112

South Asian (SAS) AF: 0.748 AC: 3598 AN: 4812

European-Finnish (FIN) AF: 0.804 AC: 8507 AN: 10580

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.848 AC: 57391 AN: 67718

Other (OTH) AF: 0.834 AC: 1757 AN: 2106

Alfa AF: 0.847 Hom.: 36378

Bravo AF: 0.863

Asia WGS AF: 0.678 AC: 2358 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.89
DANN	Benign	0.80
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs2415836; hg19: chr14-44540560;