13-34391274-T-G

Variant names:

• chr13-34391274-T-G
• rs7323331
• ENST00000605909.1:n.83-38193T>G

Variant summary

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

The ENST00000605909.1(LINC02343):​n.83-38193T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 152,064 control chromosomes in the GnomAD database, including 36,208 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 0.68 (36208 hom., cov: 32)
• Consequence: LINC02343 ENST00000605909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 3 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=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.747 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02343	NR_146542.1		n.83-38193T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02343	ENST00000605909.1	TSL:4	n.83-38193T>G		intron	N/A
	LINC02343	ENST00000664334.1		n.140-38193T>G		intron	N/A
	LINC02343	ENST00000791005.1		n.86-38193T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103354 AN: 151946 Hom.: 36187 Cov.: 32

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.680 AC: 103415 AN: 152064 Hom.: 36208 Cov.: 32 AF XY: 0.674 AC XY: 50115 AN XY: 74318

African (AFR) AF: 0.625 AC: 25916 AN: 41456

American (AMR) AF: 0.619 AC: 9460 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2664 AN: 3470

East Asian (EAS) AF: 0.194 AC: 1004 AN: 5164

South Asian (SAS) AF: 0.615 AC: 2966 AN: 4826

European-Finnish (FIN) AF: 0.750 AC: 7922 AN: 10568

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.752 AC: 51129 AN: 67990

Other (OTH) AF: 0.705 AC: 1488 AN: 2112

Alfa AF: 0.730 Hom.: 66307

Bravo AF: 0.664

Asia WGS AF: 0.503 AC: 1750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	1.0
DANN	Benign	0.62
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7323331; hg19: chr13-34965411;