rs41321845

Variant names:

• chr14-86334213-C-G
• rs41321845
• ENST00000553679.1:n.58+1780C>G

Variant summary

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

The ENST00000553679.1(LINC02309):​n.58+1780C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0222 in 152,154 control chromosomes in the GnomAD database, including 218 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 0.022 (218 hom., cov: 32)
• Consequence: LINC02309 ENST00000553679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.87
• Publications: 0 publications found

Genes affected

LINC02309 (HGNC:53228): (long intergenic non-protein coding RNA 2309)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553679.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02309	ENST00000553679.1	TSL:3	n.58+1780C>G		intron	N/A
	LINC02309	ENST00000730143.1		n.206+1780C>G		intron	N/A
	LINC02309	ENST00000730144.1		n.206+1780C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0220 AC: 3352 AN: 152036 Hom.: 213 Cov.: 32

Gnomad AFR AF: 0.00966

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.0941

Gnomad SAS AF: 0.00972

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00500

Gnomad OTH AF: 0.0278

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

GnomAD4 genome AF: 0.0222 AC: 3372 AN: 152154 Hom.: 218 Cov.: 32 AF XY: 0.0254 AC XY: 1886 AN XY: 74366

African (AFR) AF: 0.00977 AC: 406 AN: 41548

American (AMR) AF: 0.133 AC: 2018 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.00288 AC: 10 AN: 3468

East Asian (EAS) AF: 0.0943 AC: 487 AN: 5166

South Asian (SAS) AF: 0.00994 AC: 48 AN: 4830

European-Finnish (FIN) AF: 0.000188 AC: 2 AN: 10622

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00500 AC: 340 AN: 67990

Other (OTH) AF: 0.0275 AC: 58 AN: 2106

Alfa AF: 0.0109 Hom.: 6

Bravo AF: 0.0317

Asia WGS AF: 0.0500 AC: 172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.075
DANN	Benign	0.65
PhyloP100		-4.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs41321845;

hg19: chr14-86800557;