13-34428716-C-T

Variant names:

• chr13-34428716-C-T
• rs2209372
• ENST00000605909.1:n.83-751C>T

Variant summary

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

The ENST00000605909.1(LINC02343):​n.83-751C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,020 control chromosomes in the GnomAD database, including 3,564 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 0.12 (3564 hom., cov: 33)
• Consequence: LINC02343 ENST00000605909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 0 publications found

Genes affected

LINC02343 (HGNC:53263): (long intergenic non-protein coding RNA 2343)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000605909.1. 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
	LINC02343	NR_146542.1		n.83-751C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02343	ENST00000605909.1	TSL:4	n.83-751C>T		intron	N/A
	LINC02343	ENST00000664334.1		n.140-751C>T		intron	N/A
	LINC02343	ENST00000791005.1		n.86-751C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18251 AN: 151902 Hom.: 3546 Cov.: 33

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.00879

Gnomad AMR AF: 0.0526

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00290

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00304

Gnomad OTH AF: 0.0877

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

GnomAD4 genome AF: 0.120 AC: 18306 AN: 152020 Hom.: 3564 Cov.: 33 AF XY: 0.116 AC XY: 8599 AN XY: 74322

African (AFR) AF: 0.412 AC: 17039 AN: 41396

American (AMR) AF: 0.0525 AC: 802 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 38 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5176

South Asian (SAS) AF: 0.00311 AC: 15 AN: 4816

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10578

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00304 AC: 207 AN: 68000

Other (OTH) AF: 0.0868 AC: 183 AN: 2108

Alfa AF: 0.0447 Hom.: 122

Bravo AF: 0.139

Asia WGS AF: 0.0250 AC: 90 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.4
DANN	Benign	0.61
PhyloP100		0.25
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2209372; hg19: chr13-35002853;