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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02309	XR_944113.3	n.214+1780C>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02309	ENST00000553679.1	n.58+1780C>G		intron_variant	Intron 1 of 2	3
LINC02309	ENST00000730143.1	n.206+1780C>G		intron_variant	Intron 2 of 3
LINC02309	ENST00000730144.1	n.206+1780C>G		intron_variant	Intron 2 of 4
LINC02309	ENST00000730145.1	n.199+1780C>G		intron_variant	Intron 2 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs41321845; hg19: chr14-86800557;